Career transition - or destruction? - into complementary and alternative medicine

Funding at NIH is very tight this year, with a new budget that doesn't even keep up with inflation. Luckily, NCCAM (the National Center for Complementary and Alternative Medicine) is still giving out grants aplenty. I've highlighted a few of NCCAM's awards in previous posts - and will do so again - but today I thought I'd look for myself to see what kinds of funding they're offering to eager young scientists.

Well, here's one: a "Complementary and Alternative Medicine Career Transition Award" (PAR-05-129), a grant to encourage scientists to change their focus and start a career in CAM. Think of how rewarding it will be! Scientists who win these prestigious grants will have four years of support as they learn how to confuse patients and obscure the truth, so that they can be paid (sometimes well paid!) for offering sham treatments. And NIH will pay your entire salary all the while - wonderful!

I should explain that "career awards" from NIH are actually a very important mechanism for funding new scientists and for funding scientists who are making a transition to a new field. These awards are used by all the major NIH institutes, so NCCAM is just using one of the standard types of awards, but with a CAM twist, of course. You see, it's hard to find a good position doing CAM research - as NCCAM explains it:
For postdoctoral trainees doing research in CAM, this transition has an added challenge because there are still relatively few CAM departments in research institutions where they might seek positions. Therefore, an important goal of this initiative is to improve the chances of outstanding postdoctoral scientists preparing to do CAM research to obtain positions in either CAM and more conventional departments in research institutions, thus benefiting the CAM research field as a whole.... Providing support to such trainees is crucial to CAM research to ensure a sufficient number of highly trained researchers in this relatively new research field.
This selection has a number of flawed assumptions in it: let's start at the end: why do we need to "ensure a sufficient number" of researchers in a field that doesn't have any solid science to back it up? Scientific research isn't about sustaining any field for its own sake - research that gets results will grow naturally, and research that fails will shrivel away, as it should. Happens all the time. In fact, unless a field has money specially earmarked for it, the peer review process makes it very difficult to obtain funds for poorly designed research or, worse, pseudoscience. This is why we need to eliminate NCCAM.

So what kinds of research does NCCAM want the eager young researcher to pursue? Well, they state that CAM research is in "four major domains: mind-body medicine, biologically based practices, manipulative and body-based practices, and energy medicine." Since all of these "domains" are various forms of quack medicine, many scientists probably don't know exactly what they are - after all, our "conventional" training doesn't cover quackery. (Medical schools, take note! Your curricula need to be expanded.) But NCCAM is ready with some definitions, such as this page for energy medicine, which explains that there are two types of energy fields:
1. Veritable, which can be measured
2. Putative, which have yet to be measured

Yes, you read that right! NIH is funding research into energy fields that cannot be measured! Or to use NCCAM's phrase, that "have defied measurement to date by reproducible methods." NCCAM includes in this category the following types of "energy": qi (Chinese), ki (Japanese), doshas (Ayurveda, see my blogpost on that), prana, etheric energy, fohat, orgone, odic force, mana, and homeopathic resonance.

I couldn't make up better nonsense even if I were trying. But other people believe this stuff, so shouldn't we respect it? No! Does it deserve our scorn and derision? Yes! Scientists are harsh critics even about legitimate science, and we certainly shouldn't go easy on garbage like this. Actually, part of me wonders if someone at NCCAM put together this site as a sort of cry for help - it's like they're asking for someone to point out its ridiculousness.

So, young Jedi scientist, fire up your computer and write a proposal to NCCAM to study the force, or qi, or odic force, or whatever. Real science is much harder - you have to conduct experiments with reproducible results! Why bother when you can just make stuff up instead?

And finally, a postscript to anyone who's read this far and is thinking of applying for one of these NCCAM grants: if you want to try something really subversive, propose to do your postdoc training in my lab. You can "apply rigorous research methods to investigate the efficacy and underlying mechanisms of CAM therapies," exactly as NCCAM requires. I'll work with you to debunk as many claims as we can. And if at the end of a year you determine that it's all bunk, at least some of NCCAM's money will have been well spent.

A tiny drop of ink, a big win for science

Buried amidst the bad news on the budget today is this gem from Rick Weiss of the Washington Post:
It is barely a drop of ink in the gargantuan omnibus spending bill ... a provision that would give the public free access to the results of federally funded biomedical research represents a sweet victory for a coalistion of researchers and activists who lobbied for the language for years.

What this means is that after years of battling the publishers' lobby, patients' advocates and scientists have finally won a victory, even if it's not everything we wanted. What did we win? The language buried in the giant spending bill will require NIH-funded researchers (like me) to make their published research freely available to the public within 12 months of publication.

This is very good news, and the patients' advocates deserve the most credit. Thanks to the Internet, patients have discovered that they can read about the latest research on treatments for their conditions - cancers, infectious diseases, environmental hazards, and more. These same patients have discovered, as scientists have known for years, that most journals won't give you access to anything more than a title and abstract (and sometimes just the title!) unless you pay a heft fee, typically $30-$50 or more per article. These fees are truly unfair, even ridiculous, for work that was funded by the taxpayers in the first place. Patient groups have expressed growing outrage that they can't even read the research that they paid for - research that, in many cases, offers them the only hope they can find for a cure.

A recent statistic showed that a typical NIH-funded publication cost the taxpayers over $150,000. How could it possibly be that private publishers owned the copyrights to any of these studies? But they did, mostly because it's been a long tradition that scientists signed over copyright when they published in a journal, and the funders (usually the government) allowed them to. Believe me, scientists don't want to sign over copyright - it's just that we had little choice until the Internet came along, and more recently the emergence of open-access journals. Even today, though, despite the growth of open access, many of the leading journals in science and medicine are not open access, and their subscription fees are often exhorbitant. [As an aside, the Wash Post reports that the average scientific journal subscription has risen to over $963 per year, a cost that more than doubled since 1995.]

The new system isn't perfect: journals will be allowed to keep results under lock and key for up to 12 months, restricting access. This was a compromise that I hope we can improve upon. The original proposals called for either immediate access or a 6-month delay, but publishers and their lobbyists were able to get this changed to 12-months. Those of us who follow Washington politics know that NIH almost made this their policy over two years ago - but at the time, the lobbyists somehow got to the NIH Director (Zerhouni), who at the very last minute made it "optional." So of course the journals refused to change their practices and nothing changed at that time.

This new free access policy is a big breakthrough. Thanks and kudos to the citizens and scientists - many of them working tirelessly behind the scenes for the past several years - who finally succeeded in opening up scientific research to the public. Now let's work on reducing that 12-month delay to zero.

Time magazine's top 10 discoveries of the year: fooled by Craig Venter

So Time magazine has a list of its choices for "top 10 scientific discoveries of the year". We all love these top-10 lists - they're fun. But they made a huge error on one of them, so I'll make a small, probably futile, effort to correct it here.

Their #2 discovery is "Human mapped", which refers to Craig Venter's publishing his own genome. I blogged about this before, pointing out that PLoS Biology was lowering their standards by publishing that paper, which had virtually no novel scientific content. But Time reports breathlessly that the publication was "the first such genome ever published" of " all the DNA in both sets of chromosomes inherited from each of his [Venter's] parents." But was it?

No - of course it wasn't. If the Time reporter (Krista Mahr) had actually read the paper rather than the press releases, she'd have learned that the paper describes just one set of chromosomes - not two. In fact, Craig published a mishmash of his chromosomes, with bits and pieces of each chromosome merged together in a mosaic. (This is exactly what we did in the original human genome papers, by the way.) The only slight contribution of this year's paper was to fill in some of the gaps, and in some cases to separate the haplotypes (the two chromosomes) enough that, as I wrote in my original blog, they could claim that blocks of 200,000 bases on average came from a single chromosome. What does that mean? It means that in in the genome they published, each chromosome is a composite sequence containing many bits and pieces of both the parental chromosomes. For chromosome 1 there are over 1000 of these chunks, for example, and there is no information (in Venter's paper) about which chunk comes from which parent.

Furthermore, because Venter and colleagues didn't sequence his parents, they have no idea which parent any chunk came from. In other words, Venter did not publish his entire diploid genome: that would imply he published two copies of each chromosome, one from his mother and one from his father. Am I being clear here? Time magazine got this wrong, as did some of the original press reports.

Having worked with Craig for years and observed much of the press hullaballoo that he works so hard to generate, I'm not surprised that Time got this wrong. Craig is the main source of the misinformation: if you go to his institute's website today, as I did, the front page has a big image of a human karyotype (showing two copies of each chromsome), with the text below saying "New individual human diploid sequence." Sure sounds like there are two sequences for each chromosome, doesn't it? And the front page also has a link to a press release about the paper titled, "First individual diploid huma genome published by researchers at J. Craig Venter Institute." The press release goes on to refer to "six billion base pairs from the genome of one person." It also says that "the publicly funded genome ... is a composite version," implying that Craig's is not.

Obviously the Time reporter is reading the press releases: if you go to PLoS Biology and look at the paper, the second sentence of the article says that the genome comprises 2,810 million bases. If anyone is counting, that's just under 3 billion, not 6 billion. The paper also makes it clear that Craig's parents were not sequenced, so there is no way to tell which parts of any chromosome came from which parent.

Clearly Craig is trying to re-write scientific history by press release, and he might even get away with it. I claim that it is scientifically dishonest for him to have these misleading statements on his institute's website. If Time magazine were to look at the actual scientific paper, they'd realize that this item on their top 10 list is sloppy journalism, and an unfortunate mistake.

Let's be clear here: the Venter Institute's own press release says
"Independent sequence and assembly of the six billion base pairs from the genome of one person..."
but the paper reports 2.81 billion bases. That's not six billion. And that is misleading. I think we can get the public excited about science without lying to them - and it's too bad that it succeeded (this time) in getting Time magazine to report a "discovery" that didn't happen.

Damn, I lost another 4000 genes!

Where do those genes keep going? Just a few short years ago, we were arguing about whether the human genome had 100,000 genes or maybe just 80,000. Then we published the human genome ("we" being about 2000 co-authors on 2 papers) and reported that alas, we only had 25,000-30,000 genes. What a let down. The lowly weed Arabidopsis thaliana has 25,000 genes - can't we do better than a plant? It doesn't even have a brain, for pete's sake!

Well, don't look now, but a new study by Michele Clamp and colleagues at MIT's Broad Institute, just published in PNAS, says that the number, which had been hovering at 24,500, should be reduced to 20,500. Their analysis is pretty convincing - they did careful alignments of all human genes to both mouse and dog, and were able to identify several thousand genes that didn't seem to exist in our furry friends. Wait, though, you might say: perhaps these are specific to humans, or at least to primates? No, they thought of that too, and virtually none of the "genes" they propose deleting were found in our chimpanzee cousins either. That means that either we just delete these genes, or accept the rather far-fetched hypothesis that primates have both a "prodigious rate of gene birth" (to allow for over 1100 human-specific genes) and a "ferocious rate of gene death" (to explain why we don't see a similar number of genes shared by humans and chimps but no other species).

They eliminated quite a few other genes on the way to reducing the gene count by 4000, and I must admit their methods are pretty compelling.

So it appears that we have to take ourselves down another peg. We still have more genes than fruit flies, but the gap is getting smaller. I've been telling my students that size doesn't matter - we don't have the biggest genome, we don't have the most genes, we're not the biggest creatures by a wide margin. And lately we've learned that our own bodies have more bacterial cells (by a factor of 10 or more!) than human cells.

We humans want to think we're tops at something - wait, I've got it: we have the biggest egos! But those darn cats, now, I don't know...

Stem cell triumph

It's always exciting to hear about scientific breakthroughs, and the news today is truly remarkable: scientists at two different places (the Univ. of Wisconsin and Kyoto Univ.) have managed to turn human skin cells into embryonic stem (ES) cells. This has been the "holy grail" of stem cell research for the past ten years, and until today it wasn't at all clear when it would be achieved. The media is full of the news, and rightly so.

The promise of these ES cells is fantastic, almost the stuff of science fiction. With re-programmed ES cells, we should be able to grow replacement tissues for almost any organ in the human body, using a person's own cells as a source. By using your own cells, the problems with organ rejection that plague transplant patients are eliminated. I predict that, once this becomes reality, the first attempts will be to replace non-critical tissues such as cartilege (my knees could use it!), and if those are successful, we'll move on to growing replacements for things like kidneys, livers, lungs, and heart tissue. This is likely years away, but it really does seem feasible now. And of course - though none of today's news stories seem to mention this - the hope of life extension through permanently young organs seems much brighter now.

Of course, there are many caveats. This is basic research, not clinical practice, and the first problem is that both groups used retroviruses to transform skin cells into ES cells. The idea is simple: retroviruses insert themselves into the host DNA, so the two groups (Shinya Yamanaka in Kyoto, James Thomson in Wisconsin) each identified four genes that seemed to be able to turn normal cells into ES cells. Intriguingly, the two groups used four different genes - Yamanaka used oct3, sox2, klf4, and c-myc, while Thomson used oct3, sox2, nanog, and lin28. (See their papers in the journals Cell and Science for details.) They created one retrovirus for each gene, and then infected skin cells with all four retroviruses. The result is that some skin cells, about 1/10,000, got all four extra genes (of course they already had one copy of each gene), and purely by chance the genes were inserted into their genomes in such a way that they turned on. The randomness of the method is one thing that needs work - if a retrovirus inserts in the wrong place, it will disrupt normal functions, and the resulting ES cells will be defective.

I've already been asked whether this means that we can abandon research on human embryonic stem cells created from fertilized human eggs - this is the research that President Bush and other conservative Republicans have opposed, based on religious reasons. The answer is a resounding no, as Thomson already said. Among other things, we need "real" ES lines to be able to determine if the new ES cells are truly pluripotent; that is, to see if they're as good as the real thing. One should always be very skeptical when politicians - especially politicians as anti-science as Bush - make assertions about the implications of any scientific result. (An aside: I'm a member of the Maryland Stem Cell Commission, which determines how to allocate the state funding that my state has set aside to promote human ES research, but I don't do stem cell research myself and I'm not eligible to receive these funds.)

These and other caveats aside, though, today is a good day for science. What a great way to start the Thanksgiving holiday in the U.S., with real hope for the future.

Flu vaccine blunder

I got my flu shot - did you get yours? Well, you should.

There, now that I've said that, I can explain why the shot might not do you any good. Unfortunately, the CDC (Centers for Disease Control) and WHO (World Health Organization), who jointly decide what flu strains to put into the vaccine each year, may have made a serious mistake this year. I don't want to criticize these organizations, which do wonderful work each year that benefits public health in countless ways, but if I'm going to be consistent, I can't keep silent when I see a mistake, even if I like the organization(s) behind it.

The short version of the problem is that the CDC/WHO panel decided to put the same strain of H3N2 (the most common type of human flu) into the vaccine this year as we had last year. They made this decision despite the fact that the data clearly showed that a new H3N2 was emerging. The consequence is likely to be - I fear - that those of us who get the flu shot will have almost no protection against this year's flu. Not good.

Some background: the flu shot has 3 strains in it: H3N2, H1N1, and influenza B. Last year was a mild season dominated by H1N1, which is usually mild. The CDC/WHO committee decided to replace the H1N1 in the shot, using a recent isolate - so if you get the shot, then at least you're protected against H1N1. However, H3N2 is dominant in most years, and "bad" flu years are always H3N2-dominant. Why do I say a new strain was emerging? Well, here is some of the data:In this chart, which shows flu cases throughout last season (2006-7), the blue bars indicate H1N1 cases and the red bars show H3N2. (Yellow bars are untyped, so we don't know what those are.) Notice that through the middle of the season, which was in mid- to late-February, H1 was dominant. But in the later part of the season, from March on, H3 became dominant, and by late March almost all the cases were H3N2. Clearly, H3N2 was taking over again.

The WHO's own report on this data admits that a new strain was emerging. So why did they choose an OLD strain - from 2005, no less! - for this year's vaccine? Here is what their report says: "An increasing proportion of isolates was distinguishable both antigenically and genetically from the vaccine strains; however, antigenic analysis did not reveal the emergence of a sufficiently well characterized antigenically variant group." In other words, the new isolates were clearly different from the vaccine strain (A/Wisconsin/67/2005), but they weren't sure which of the new isolates was going to be the new one. They also reported that "the lack of egg isolates precluded the selection of a new vaccine candidate"; in other words, they weren't sure if they could grow the new isolates in eggs, which is how we make vaccines here in the U.S. (Using eggs is an outdated system that must be changed, but I'll have to save that topic for another blog.)

So the bottom line is that: (a) they knew that a new strain was emerging, (b) they weren't sure if we could grow it in eggs, and (c) they weren't sure which of the new isolates was the best choice for the vaccine. So they decided to put the old strain in the vaccine, even though they knew it was ineffective. In fact, their own data show that it was only effective in about 34-58% of cases last season - a number that is likely to be much lower this year.

Part of the problem is that the panel that chooses the flu vaccine strains continues to rely heavily on traditional serotyping methods rather than the newer, more precise genotyping methods available through influenza genome sequencing. A related problem is that the CDC doesn't release its influenza genome data, as I and others have pointed out in the past. (See our letter to Nature on this topic from March 30, 2006 - despite numerous calls to release data immediately, the CDC and WHO still sit on their flu data, often holding it for years.)

Why doesn't the CDC release flu genome data immediately? Part of the problem, though they won't admit it, is that they don't want to be second-guessed by "outsiders" on what strain to put into the vaccine next year. The data used to make this decision should have been available last winter, but the CDC only shares it with three other WHO collaborating centers (more info here). Of course they are trying to do the right thing - to choose the right vaccine strain - but they shouldn't be afraid of hearing the advice and opinions of other scientists who might disagree with them.

Still, get your flu shot. Maybe we'll get lucky and we'll have another H1N1 flu season. I hope so.

Lousiana elects a new governor: why does "conservative" mean "creationist"?

As a computational scientist and an evolutionary geneticist - and a professor - it pains me to see how many conservative politicians in the U.S. seem to believe in the anti-scientific Creationist view of life. This is currently promoted under the thin disguise of "intelligent design," but that isn't fooling anyone. Creationists (and intelligent design-ists) believe that the world and everything on it was created by a divine being some 6000 years ago. They simply ignore the enormous body of scientific evidence showing that species evolve through the process of natural selection, which has been going on for several billion years.

But today's topic is the election in Louisiana of a new governor, a conservative Republican named Bobby Jindal. Most of the news stories (for example, the NY Times) have focused on the fact that Mr. Jindal is the first-ever Indian American elected as governor of any state. The stories have also mentioned that the "social conservative" believes in teaching intelligent design instead of evolution in our public schools.

Stop right there. Does everyone in the conservative (Republican) movement in the U.S. believe the world was just created - poof! - by a magic puff of smoke just a few thousand years ago? Does becoming conservative mean that you cannot understand simple scientific evidence - even overwhelming evidence? Evolution is probably the most well-supported scientific theory in all of biology, with 150 years of accumulating evidence backing it up. It has changed over the years - a fact that some creationists use misleading to make it appear that evolution is on shaky ground - but the changes have deepened and strengthened the theory, not weakened it.

The genome sequencing work I've been involved in over the past dozen years has provided some of the strongest evidence yet about how species evolved and are continuing to evolve. The molecular evidence for evolution is just spectacular.

So I'm dismayed that Mr. Jindal promotes a view that will undermine science teaching in our schools. He isn't the only national figure that believes this (George W. Bush has also supported the teaching of creationism - it's hard to know if he is sincere or just pandering, though), but we need to start calling people out when they make ignorant statements.

So I'm asking for those of you who call yourselves "conservative" to start speaking out on behalf of evolution - and science in general. If you're a conservative (and I'm not, if that isn't obvious already), you should be embarrassed to be associated with the ignorant, anti-scientific drivel that "intelligent design" supporters spew out. Let me ask it another way: does "conservative" mean "anti-education" or even "anti-knowledge"? I hope not.

Oh great, more "alternative medicine" funding from NIH

Just before the Nobel Prizes were announced this week, NIH posted a delightful press release on its website announcing three new Centers of Excellence in Research on Complementary and Alternative Medicine (CAM). Great! I'm so excited to hear that NIH is pouring more money down this oh-so-promising black hole of negative results and poorly conducted studies!

Now, I can just hear the CAM-fans protesting: "why are you opposed to doing studies of our methods? Are you afraid that studies will prove some of them work?" (This isn't a straw man argument, by the way - I've been asked precisely this question.) Well no, of course I'm not afraid that studies will prove that [acupuncture - homeopathy - naturopathy - Ayurveda - chiropractic - voodoo] will work. There are so many problems (with this CAM announcement) that I don't know where to begin, but one major problem is that studies have already been done, and all the results are negative. As CAM's acting director, Ruth Kirshstein, writes in her request for over $121 million for next year's CAM budget, NCCAM has supported research at more than 260 institutions over the past 7 years. Have any positive results emerged? No. Why throw good money after bad? We shouldn't.

Some of my blogosphere colleagues have already put forward some excellent arguments for why NCCAM's funding should be eliminated - see the recent post by Steven Novella, who argues:
Why can’t studies of CAM modalities be funded through the regular NIH? Because the NIH has standards, and what passes for research in the CAM world is often so laughably pathetic that it could never mean the NIH standard and get funded. NCCAM was created to provide a much lower standard for CAM research. In other words – waste money on studies that are not worth funding when judged by the usual criteria.
I couldn't have expressed it better. If this work is any good, it will get funded through the regular NIH mechanisms. Also see the comments of ScienceZoo, who points out that none of the three new CAM Centers are likely to find effective therapies for what they claim to be studying.

While I was celebrating this announcement from NIH, I couldn't help myself (I was so excited!!!) from looking at what their existing "Centers of Excellence" devote themselves to. You can find a list here, and it includes one for acupuncture (see my previous post on that topic), energy medicine (what the heck is that? I'll blog on it another time), and "mindfulness-based stress reduction" in HIV.

That last one is really rather appalling: they will investigate using meditation techniques as a way to "slow disease progression and delay the need for antiretroviral treatment." So they're going to tell HIV-positive patients to delay taking proven therapies and try meditation instead? How many patients need to die before they admit this isn't a good idea.

So you see, we have so much to celebrate this week. Three new NCCAM centers and a request for another $121 million in NCCAM funds next year. I'm so happy.

Fake acupuncture works as well as "real" acupuncture

I haven't looked at acupuncture in this space yet, but a recent study in the Archives of Internal Medicine provides some entertainment - and food for thought. The authors, Brinkhaus et al., compared the treatment of lower back pain with "real" acupuncture to two alternatives: "sham" acupuncture, in which needles are placed in random locations and inserted only superficially (not as deep), and no acupuncture at all.

The study found that both sets of patients with acupuncture reported reduced lower back pain as compared to the "no treatment" group; however, there was no difference between the real and sham treatment groups. In other words, if you thought you were getting acupuncture, you reported less pain. The authors here look at this as a victory, of sorts (and they clearly believe in acupuncture themselves - raising questions of bias in the study). It's also worth noting that one of the authors has a clear financial interest in a positive outcome - he receives fees for teaching acupuncture to professional societies; and several of the authors work at centers for complementary medicine.

I'm not surprised that the sham treatment worked as well as the "real" acupuncture. However, I don't believe that either treatment really works. As with many studies of pseudoscience, the condition (here, lower back pain) is subjective and very difficult to measure. The placebo effect is obviously at work: the patients know they had a treatment, which was a painful one, and they want to believe it was worth it. A better study would have included controls who received another treatment - massage for example - rather than nothing.

Worse yet, this study is riddled with other methodological problems. First, the physicians weren't "blinded" to the treatments. In other words, the physicians knew that they were giving real vs. sham acupuncture, introducing another source of bias. A questionnaire given to patients revealed that at least some of them figured out that they had had sham treatment.

Acupuncture has been studied countless times before (sometimes with funding from our friends at NCCAM), and the best studies show, unsurprisingly to me, that it just doesn't work. (Not surprising because there is no known physiological mechanism that would allow it to work. It's just magical thinking.) Now, although meta-analyses are highly problematic themselves, the best meta-analyses are usually the Cochrane studies, so I'll mention here that there was a Cochrane study of precisely this: "The effectiveness of acupuncture in the management of acute and chronic low back pain." You can read the abstract here. They found, after reviewing many other studies, that "there was no evidence showing acupuncture to be more effective than no treatment"; in other words, it just doesn't work.

I was interested to see that Brinkhaus et al. mentioned the Cochrane study above, but dismissed it and said that more recent studies supported their opinion that acupuncture (sham or real) is better than no treatment at all. They cited a more recent (2005) Cochrane study as one of these. But ironically (or should I say "blindly" on the part of Brinkhaus et al.?) this new study did not find evidence that acupuncture works at all. The newer Cochrane study found that almost all the studies were of low quality, and that "the data do not allow firm conclusions about the effectiveness of acupuncture for acute low-back pain." But that didn't stop Brinkhaus et al. from asserting that there is an effect. As long as they study hard-to-measure phenomena like pain, with poorly designed experiments, they'll continue to be able to find weak effects and then claim that "more research is needed."

So, if you want to enrich your local alternative healer, by all means let him stick you full of needles. But if you want to feel better, there are much more pleasant choices that won't cost you a thing.

NIH and Ayurveda, part 2

Another in my continuing series on some astonishingly stupid research funded by NCCAM, the NIH center for sham medicine (oops, I meant "alternative" medicine). This post looks at grant R21AT001969, to Cathryn Booth-Laforce at the University of Washington in Seattle, titled "Ayurvedic Center for Collaborative Research."

If you thought I'd picked out a couple of oddities in my previous posts on the pseudoscience funded by NCCAM, I'm afraid - sadly - that you're mistaken. There are plenty more examples, of which this project is just one. This project will spend thousands of your hard-earned tax dollars to set up a center for collaboration between the PI's university and a place called The Ayurvedic Trust in India, supposedly to conduct research projects. However, this nice-sounding goal ignores the fact that Ayurvedic is little more than a set of ancient superstitions, founded on ignorance and magical thinking, with no scientific merit to any of them. I recommend the article on Ayurvedic mumbo-jumbo at for those who are interested.

A quick primer: in Ayurveda, all of the body's functions, including health, sickness, and so on, are regulated by three "doshas", which are really quite meaningless from a scientific point of view. For example, the dosha called vata "governs all bodily functions concerning movement" and accumulates during cold, dry, windy weather. Is there any basis for this? No. What's worse is that Ayurveda "medicines" (I have to put that word in quotes here) contain well-known toxins such as mercury, arsenic, and lead. In fact, a scientific study in the Journal of the America Medical Association (Saper et al., JAMA (2004)292:2868-2873) found:
One of 5 Ayurvedic HMPs [herbal medicine products] produced in South Asia and available in Boston South Asian grocery stores contains potentially harmful levels of lead, mercury, and/or arsenic. Users of Ayurvedic medicine may be at risk for heavy metal toxicity, and testing of Ayurvedic HMPs for toxic heavy metals should be mandatory.
What is a bit unusual about this grant is that the PI, Dr. Booth-LaForce, is a professor of nursing at a highly regarded university. Her bio reveals the source of her interest in Ayurveda: "she is studying yoga and Ayurveda-based meditation as possible therapies for menopausal symptoms." Well, I'm not exactly sure what Ayurveda-based meditation is, but I'm pretty certain it isn't science.

Ayurveda isn't medicine, and it isn't "complementary" to medicine either. NIH shouldn't fund it, no matter who the PI is. Research dollars are too precious to waste, and NCCAM should be shut down.

PLoS Biology, vanity publisher?

I'm a big fan of open access, and I'm rooting for PLoS Biology to succceed in their goal to publish papers that have the same quality and impact as Nature and Science. Today, though, I find myself both surprised and disappointed, as PLoS Biology shows that its hunger for publicity threatens to turn it into a vanity publisher.

You see, in an article appearing tomorrow morning (4 Sept 2007), PLoS Biology is publishing a paper by Craig Venter and colleagues about....(pause)... Craig Venter's genome! So when I get enough money to sequence my genome, will PLoS Biology publish that too? Is this the Donald Trump-izing of science?

But wait, you might object - maybe there's some science in the paper. Well, first you might want to recall that the original human genome paper published by Celera, in early 2001, was predominantly based on Venter's DNA, as he later admitted in a letter to Science. (Disclosure: I worked with Craig and was a co-author on the 2001 paper, and I fully stand behind it.) So most of the science was published over six years ago.

Still, I have the paper here and I've read it, and I can re-assure you that there isn't anything new, unless you are interested in how many differences there are between Craig Venter's genome and the reference human genome (the one in Genbank, which is very nearly complete). If anything, it's kind of a weirdly voyeuristic read, in which you an learn details of Craig's family history (English ancestry, three siblings, etc.), and you can see a full-page picture of his karyotype. Then there's a lengthy description of how they compared the genomes and found all the differences, but I confess I couldn't go on beyond page 10. In what I read, there wasn't much new science, certainly not of the caliber I've come to expect in PLoS Biology.

PLoS Biology will probably get plenty of attention for this paper. In politics there's a saying: any publicity is good publicity. In science, though, we think otherwise. PLoS: why'd you have to do this? I guess I shouldn't have expected so much of you.

NCCAM and homeopathy

Some of those who read this blog might wonder if there are other examples of pseudoscience and quackery supported by NIH's National Center for Complementary and Alternative Medicine (NCCAM) beyond the study on magnetic field therapy I pointed out back in June.

Unfortunately, there are lots of examples. I'm going to highlight a few more in the coming weeks, starting today. As I've written before, NCCAM is an embarrassment to NIH - it funds research that never would have made it through the rigorous review at other NIH institutes, and it is a waste of money. NIH should shut it down.

Today's example is a triple play: three grants all funded by NCCAM to the same investigator, Professor Iris Bell at the University of Arizona, who is a big fan of the homeopathy, a pseudoscience that I and many others have written critically about (see the Homeowatch site, for example).

The first one (grant R21AT003212) is called "Dilution and Succussion in Homepathic Remedy Dose-Response Patterns." This study, which should have been laughed out of the review panel, proposes to measure the effect of "succussion" on homeopathic remedies. Succussion is just shaking - you mix the stuff in, shake it up, and then dilute it. As I've explained before, homeopathic dilutions reduce the amount of "active ingredient" (usually an ingredient that doesn't provide any benefit anyway) to zero - literally so, because the dilution is so great that there is almost no chance that even a single molecule of the original substance remains, so all you have is water. Bell argues (as other homeopaths have recently) that the water retains a "memory" of the substance, and that this water still has a beneficial effect. There is no physical theory - and no evidence whatsoever - to support this claim, but there it is, right in the abstract of this grant. Dr. Bell hijacks the language of real science - clinical trials - to propose a randomized trial of various dilutions with "stirring only" versus 10, 20, or 30 succussions - that is, shakings. So NCCAM will fund a study that will compare several variants of a completely ineffective "potion." Dr. Bell isn't even going to test its effectiveness on a specific ailment - instead, she proposes to test how well subjects can "sniff" the different preparations. This is, frankly, ridiculous.

Grant number 2 to Dr. Bell is R21AT000388, "Polysomnography in Homeopathic Remedy Effects." This one will test the effects of two plant extracts on people's EEGs while sleeping (and compare them to a placebo). Both extracts will be given in 30c doses. "30c" means a dilution of 100 raised to the 30th power, or 1 followed by 60 zeros - in other words, the subjects will be given water that has a near 100% chance of containing not a single molecule of the plant extract (one of which comes from a coffee plant). The argument for using coffee is homeopathy's "Law of Similars" - that (quoting from the grant itself) "a substance that can cause symptoms in a healthy person can cure similar symptoms in a sick person." Luckily for the subjects, they won't actually get any coffee before bedtime, because the homeopathic potion won't contain any. Again, this should have been laughed out of the review panel.

Grant number 3 to Dr. Bell is 5K24AT000057 (and she has a 4th grant from NCCAM too), "Individual Differences in CAM Patient-Centered Outcomes", is already in its 8th year of funding. This doesn't have very specific aims, but instead supports "a program of research to understand the nature of global and multidimensional whole person healing patterns within homeopathy as a whole system of CAM."

None of this work should be funded with precious NIH research dollars. NCCAM undermines the credibility of all the terrific work going on in other institutes, and it drains precious funds from other studies where those funds would contribute to real science. Congress and NIH should shut it down.

Religion in the journal Nature

Kudos to Sam Harris - author of The End of Faith - for writing a letter to Nature (Nature 448, 864, 23 August 2007) criticizing the editors of Nature for their support of supernatural beliefs; i.e., religion. Harris first points out the hypocrisy in Nature's publication of an earlier opinion piece (in the July 12 issue) that argues that Islam has "an intrinsically rational world view." Ironically, the author of the earlier piece (Z. Sardar) acknowledges that "science in Muslim society has suffered a drastic decline," and he seems to genuinely believe that the Islamic religion is consistent with scientific thought, and that science can "reunit[e] reason with revelation." Harris points out that Islam - just like Christianity - regards its holy book as something that "cannot be challenged or contradicted, being the perfect word of the creator of the Universe" - which is a supremely un-scientific attitude. Harris also criticizes Nature for their favorable editorial about Francis Collins' recent book on his own personal religious (Christian) beliefs, and he includes some choice quotes pointing out how un-scientific that book is.

Harris' criticism of Nature is right on the mark. We are inundated with writing about religion, and religious people have a huge number of highly visible outlets to express their views. Religion is discussed daily in the mainstream media as well as countless specialized publications and television shows. We have a President here in the U.S. who constantly talks about religion, and he is supported by a fundamentalist movement that wants nothing more than to impose their religion on the rest of the country. Science, on the other hand, has a far smaller number of venues, and has much less of the public's attention. Scientific publications - especially those with a large readership, such as Nature - should focus on science and science policy. Harris is right when he says: "There are bridges and there are gangplanks, and it is the business of journals such as Nature to know the difference."

Or, to put it another way, the title of the journal is Nature, not Supernature. If the editors of Nature want to publish articles about supernatural phenomena, they should change the title of the journal.

Universities should support open access to literature and medicine alike

Gavin Yamey has a thought-provoking commentary over at the PLoS blog site, in which he argues that open access to the scientific literature is related to access to essential medicines. One of the points that I agree with is that our system - indeed, even the very notion - of intellectual property rights is preventing both the dissemination of knowledge and of valuable medical treatments.

We scientists publish our work primarily so that it will be disseminated as widely as possible. (Yes, I know that we also publish so that we can get promoted in our jobs, increase our funding, and other less noble goals.) To that end, open access publishing, which puts no barriers in the way of the interested reader, is the best system from the consumer's (reader's) point of view. Even more important, in many cases, is that open access publishing allows the author to retain control of the intellectual property in the article, which is logical enough since the author created it in the first place. It never made sense to me to sign over copyright to a publisher, but publisher's were able to extort these rights from authors when they controlled the means of distribution.

As Yamey points out, access to drugs is restricted in a different - but closely related - way, through patents. I've made arguments against patents before - particularly against patents on software, which I've argued should be abolished (see my editorial here). Drug patents, despite the arguments made by the pharmaceutical industry which has a huge vested interest in the current system, are "impeding the world's poor from accessing live-saving medications," says Yamey. He's right - and more than that, they encourage drugmakers to invest only in blockbuster drugs - not necessarily drugs that cure mankind's greatest ills, but those that make the most profit - and then to invest even more in legal strategies to extend their patents and prevent competition.

Where do our universities sit in this argument? Sadly, in the U.S. at least, universities have been filing 1000's of patents a year. Starting in 1980, when Congress passed a law (the Bayh-Dole Act) encouraging universities to commercialize their discoveries, the growth in university-driven efforts to protect intellectual property has been enormous. On the whole, I believe these efforts have been harmful, because they directly contradict the mission of universities - and scientists - to disseminate knowledge.

Fortunately, there is now a group, Universities Allied for Essential Medicine, that is at least making an effort to pressure some universities to recognize the harm they're doing, and to stop it. They've called on the Univ. of Wisconsin, which has an unusually aggressive licensing arm (called WARF), to demand that Abbott reintroduce a drug that they have withdrawn from Thailand over patent disputes. (WARF owns rights to the drug.) The University of British Columbia has actually drafted a new IP policy that will guarantee access to UBC inventions in the developing world (read it here).

For now, US universities are followers, not leaders. I encourage anyone in academia to pressure your administration at every opportunity to encourage free dissemination of knowledge, through open access and through rapid, unrestricted publication of discoveries - without patents. I'm trying this already at my own institute, the University of Maryland. Not surprisingly I'm meeting resistance, but I will persist, and I hope others will join me.

One thing we professors can do on our own is to halt the practice - common in some disciplines - of counting patents as publications. I've seen many resumes with patents listed, and I don't consider these to be equivalent to publications at all. For one thing, patents aren't peer-reviewed, but are reviewed by an overburdened patent office that lacks expertise in most disciplines. For another, patents are often written to conceal the true invention, so as to discourage others from trying to re-create it. Let your colleagues know that patents don't count in promotion cases, and they'll have less incentive to file them. This is just a small step, but I think it's be a step in right direction.

the first complete eukaryotic genome?

In science news this month, a paper in BMC Biology is reporting (Nozaki et al) the sequence of "the first nuclear-genome sequence for any eukaryote that is 100% complete." This might come as a surprise to many scientists, even genomics experts.
The new genome is the red alga Cyanidioschyzon merolae, and it is just 16,546,747 nucleotides long, including all 20 chromosomes from telomere to telomere. The genome had been published previously, but it had 46 internal gaps (totaling 46,469 nt) and the telomeres were missing. They also discovered that about 20 kilobases were mis-assembled previously, a common problem that I've written about elsewhere (see my editorial with Jim Yorke, "Beware of Misassembled Genomes", available on my home page.)

But wait a minute, you might ask (as I did). What about the yeast genome (S. cerevisiae), originally published in 1996 as the first eukaryotic genome? I thought that was finished some time ago. It's true that there have been many published corrections since 1996, but I know the telomeres are present on most (all?) of the chromosomes. And how about the nematode C. elegans - it was published in 1998 while still incomplete, but about four years later it was announced as complete (see the link). These papers are cited by the new paper, but oddly, it doesn't explain what is missing from these earlier "complete" genomes. And I think we finally finished the malaria parasite, Plasmodium falciparum, although the original paper (which I was a part of) appeared in 2000, before all the gaps were closed.

Of course, most genomicists know that the human genome is still far from complete - all the telomeres and centromeres are missing, and there are several hundred other gaps - but I am a bit skeptical of the claim here that the red alga C. merolae is the first complete eukaryote. Can anyone out there tell me why I'm wrong?

Politics trumping the U.S. Surgeon General on stem cells, Plan B, and more

The Washington Post reports today (July 11) that Richard Carmona, the former surgeon general of the U.S. from 2002-6, is now saying that he was "muzzled" on numerous sensitive public health issues. He is quoted saying that the Bush administration's political appointees "ignored, marginalized, or simply buried" any medical or scientific information that didn't fit their ideology.
This is simply amazing coming from a Bush appointee. We all know that Bush and his staff carefully vet their appointees to make sure they hold politically "correct" (i.e., very conservative) views that mesh with Bush's own. It turns out that Carmona, a surgeon and former professor at the University of Arizona, is just too well educated to fit the bill, and he is now speaking out - now that he no longer works for the administration. (It's too bad he didn't speak when he was the surgeon general - Bush might have fired him, but it would have gained more attention.)
Among other issues, Carmona it clear that he supports research on human embryonic stem cells - a vital issue in medical research, which is being held back because of Bush's policy prohibiting federal funding for this research. Carmona says this issue and others was determined by theology, and by "preconceived beliefs that were scientifically incorrect." The Wash Post reports that Carmona was told simply to shut up about stem cell research when the debate was being engaged nationally.
He was also muzzled on other issues, including the "Plan B" pill that induces a miscarriage and birth control. On the latter issue, he was told not to speak out on the "abstinence only" education policy that the administration insists on, even though the scientific research makes clear that abstinence-only education doesn't stop teenagers from having sex (as if it ever would).
It's too bad that we have an administration in the U.S. that ignores science and lets theology and ideology rule over such critical issues affecting human health. But I'm pleased to see another prominent former official - one with scientific expertise - speaking out in opposition.

Disappointing science funding

Many of us in the scientific research community are hoping that with the Democrats in charge of the U.S. Congress, we might see some of the recent budget cuts to science being restored. Alas, that doesn't look likely. The new Senate proposal for the NIH offers only a 2.8% increase, which is less than inflation and therefore represents a slight cut in real dollars. At least it is better than the Bush administration's proposal, which calls for a $279 million cut in the NIH budget. The House's proposal calls for an increase, but less than the Senate, and the likely result will be somewhere in between. NSF is doing much better - after years of basically flat budgets, it seems that Congress is going to give it a 10% boost, which is a real increase. The Bush administration supports the increase to NSF - surprisingly (to me).
More fundamentally, though, I am continually dismayed by the anti-intellectual, and often anti-science, attitude of many politicians, especially those on the right. They attack science whenever it seems to conflict with their political or religious agendas, most notably on global warming and stem cell research. As a result we have a U.S. population that is stunningly ignorant of basic scientific principles, with a majority still believing in such ridiculous things as the creationist myth that all living things were magically created a few thousand years ago.
I hope this changes, but I don't see it happening soon. I'm pleased that some in Congress and even in the Bush administration want to increase certain areas of science funding (NSF, at least). I hope the public will once again see science as offering cures for disease and the means to a better life, as I think they did in the past. Or is that just my rosy view of society in an era before I was born?

NCCAM and NIH support "magnet field therapy"?

My recent blog on Ayurveda and NIH, which was mostly about NCCAM (the National Center for Complementary and Alternative Medicine at NIH), has been getting a lot of attention, so I'm starting a new thread here. Some of the responses I'm getting seem to think it's a good idea to fund "alternative" medicines. I would argue strenuously that this is not so. NIH funds research based on scientific evidence - there is no such thing as "alternative" science. Likewise, the phrase "complementary and alternative medicine" is misleading because it uses the term "medicine" - but all modern medicine is based on well-grounded, firmly established scientific principles. If an herbal extract is effective at treating a disease, then it's a medicine - not an "alternative" medicine. If it doesn't work, then it's just an herb.
So I did a quick search of what NCCAM is funding, and picked one (yes, I'm picking on one) grant to show the kind of crap they support. Here it is: NCCAM grant R21AT003293-01A1, "Carpal Tunnel Syndrome and Static Magnetic Field Therapy." The investigator, Agatha Colbert, is at a place called the Helfgott Research Institute. She wants to study whether "magnetic field therapy" can treat carpal tunnel syndrome - yes, that's magnets. There is no evidence at all that magnets cure any disease, including CTS, but that doesn't matter for an NCCAM award, apparently.
I suppose I could launch into a diatribe about the superstitions surrounding the use of magnets as therapy, but I'll avoid that. There isn't even a mechanism by which magnets could work - this is just magical thinking. Proponents of magnets sometimes say they improve blood flow, but this is nonsense - the iron in blood is not attracted by magnets (it's not in the right form for that). It's just a superstition, and having a study funded by NCCAM will do little other than allow the purveyors of "magnetic therapy" to use this as a sales tool that will help them fool a few more people with this modern form of snake oil.
By the way, the Helfgott Institute is dedicated to naturopathy, "Chinese medicine" (whatever the heck that is), and "energy medicine" (ditto). I'm sure they are very happy that NIH has set aside funds for this kind of nonsense.
NCCAM is an embarrassment.

Ayurveda and NIH

Some of you may know that our beloved National Institutes of Health has a "National Center for Complementary and Alternative Medicine" (NCCAM). This was created quite recently and as far as I can tell, is a collosal waste of precious NIH funds. This is not a victimless crime - funds spent on NCCAM could instead be spent on real NIH research, improving the prospects for curing real diseases.
Instead, NCCAM is basically a booster for "alternative" practices that are mostly complete nonsense, and in some cases are (or should be) downright embarrassing to the NIH. My topic today is Ayurveda, which I blogged about last month when I was preparing to go to a scientific conference where one of the speakers was (to my surprise) planning to speak on Ayurvedic medicine. In preparing for that meeting, I happened upon the NCCAM page on Ayurveda, here. (Yes, that's a link to NIH.)
The NCCAM site on Ayurveda goes on for page after page explaining it, and it is clear that the NIH is trying to present Ayurveda in the best light possible. This is not what NIH should do - it should support scientific investigation of health claims, not provide advertising for "traditional" practices that are little more than superstition. Despite their attempt, they can't really sanitize Ayurveda - in trying to explain it, they delve into the ridiculous beliefs of Ayurveda such as their fundamental notion that everyone has three "doshas", and imbalances in these doshas cause basically all disease. Imbalances in the first dosha - so says the NCCAM website - can make a person susceptible to "skin, neurological, and mental diseases" or with a second dosha, to heart disease and arthritis, and the third causes diabetes, ulcers, and asthma. All the doshas can be upset by eating certain types of food.
You have to scroll way, way down on the page - to point 11 - to finally come to what should be point number 1: "Does Ayurveda work?" The answer is, simply, "No." Actually the entire page should be just that question followed by that answer. But here the NIH really lets the wheels come off, and NCCAM reveals its bias: it says "A summary of the scientific evidence is beyond the scope of this Backgrounder." What??? It then makes things worse by stating that "very few rigorous, controlled scientific studies have been carried out on Ayurvedic practices. In India, the government began systematic research in 1969, and the work continues." So they are trying to suggest that this needs more study - a common ploy of pseudoscience practitioners - and even that "research" is going on today in India.
Ayurveda is harmful. If you read even further down, even the NCCAM site admits this, but only indirectly. What it says is that many Ayurvedic "medications have the potential to be toxic." (No, they are toxic.) What are they - well, even NCCAM admits that they contain lead, mercury, and arsenic. Is this accidental? The NCCAM site would leave this question unanswered, but a web search quickly reveals that Ayurveda intentionally uses these metals and others in their "treatments." So the mercury, lead, and arsenic that are found in Ayurveda potions are in fact the main ingredient.
If you really want to read about Ayurveda, check a site that presents the evidence more objectively - or skeptically, such as Unfortunately, the NCCAM site is not objective. They support Ayurveda, and other "alternative" practices, because they seem to think their mission is to be a booster for these sham practices. I think NCCAM should be shut down, and fast.

Scientists speak out against homeopathy

Nature has had a number of articles recently about pseudoscience teaching in British universities, and how some scientists are speaking out against it. Recently a group of them have taken on homeopathy, which has a long-term following in Germany and England. It is also practiced here in the U.S., though not as much.
The latest from our friends in England is an open letter by a group of scientists, led by Prof. Gustav Born of Kings College London, asking that the National Health Service stop paying for homeopathy. (Wait - can you believe this? They pay for homeopathy! What an absolutely awful waste of money.) There are all kinds of reasons not to pay for homeopathy: first, it doesn't work. Second, it encourages people to believe in a system that is anti-scientific (and doesn't work).
Steven Novella (of The Skeptics Guide to the Universe) has a blog on this topic as well, which I recommend.
By the way, if you've not heard of homeopathy, here's the 25-cent summary. Practitioners of this hocus-pocus believe that incredibly minute amounts of substances can treat symptoms. The "substances" are usually something connected with the symptom - they have a (completely unfounded) belief that "like treats like"; in other words, something that causes a symptom can treat it. So a tiny amount of the oil from poison ivy (to make up an example) might cure itching. But the belief doesn't matter anyway, because the amount of dilution they use essentially guarantees that their potions are just water. They dilute their substances so much that - no kidding - there is on average less than one molecule of the substance per does. In other words, there's nothing in it. That doesn't stop them from selling their potions to whomever is willing to pay - including the British National Health service, regrettably. By the way, I'm using the word "potion" on purpose - this is really nothing more than witchcraft. But hey, some people believe in witchcraft too. It's just that the National Health Service doesn't pay for you to go to a witch for treatment.
Good luck, Prof. Born and colleagues! I hope you can educate your own public enough to stop the waste and fraud.

pseudoscience alert

Tomorrow I'm giving a talk at a conference of the IUBS (International Union of Biological Sciences), which normally would be just an interesting scientific meeting for me. The conference is on various approaches to improving global health - my topic will be the influenza virus. However, there's a guy in my session who is giving a talk on "Ayurvedic Biology" - to which my first reaction was, "what the heck is that?" I looked into it and wrote to the session chair and then the conference chair when I found out: Ayurveda is a bunch of pseudoscientific mumbo-jumbo that has been popularized by the Maharishi Yogi and by Deepak Chopra. These guys recommend that you take minerals such as lead, mercury, gold, silver, and arsenic to treat physical ailments - in other words, they recommend that you take poison. They also use incantations, amulets, spells, and mantras. There is no scientific evidence whatsoever behind this, it's just a tradition (they say) dating back centuries in India.
There are many websites explaining it, so here's one quote: "Patients are classified by body types, or prakriti, which are determined by proportions of the three doshas. The doshas allegedly regulate mind-body harmony. Illness and disease are considered to be a matter of imbalance in the doshas." From Chopra "claims that Ayurveda works because it corrects a distortion in consciousness... Chopra repeatedly asserts that 'for every thought there is a corresponding molecule. If you have happy thoughts, then you have happy molecules.'...Chopra also asserts that masters of Ayurvedic medicine can determine an herb's medicinal qualities by simply looking at it. Scientific study is therefore unnecessary."
These guys aren't kidding! So after much effort by the conference chair - who said it was too late to invite our Ayurvedic presenter, Darshan Shankar (who turns out not to be a Ph.D. or any other type of scientist, no surprise) - we think that the chair has convinced Shankar to give a more reasonable presentation, though it still mentions Ayurveda. I hope it works, but if not I'm going to have to get up at the end and say something to make it clear I don't believe it.
This is interesting because I've never been in a position like this before. I thought about simply refusing to speak, but the conference chair put in many hours basically re-doing Shankar's slides for him, so I feel like I have to go. But we don't know if Shankar will stick to the re-written script. I'll post a followup after the conference.

the Encyclopedia of Life

The Washington Post and the Chicago Tribune had reports today about a major new effort online - to catalog every named species in a large, open website to be called the Encyclopedia of Life. This effort, inspired by Harvard biologist Edward O. Wilson, will create a Wikipedia-style site that scientists can use to enter whatever they know about every species of life. It's both incredibly ambitious and admirably realistic - the Wiki format makes this possible as long as enough people contribute.
The new project is at, and it's funded by the Smithsonian Institution, the MacArthur Foundation, Harvard University, and Chicago's Field Museum. Each species will get its own web page, obviously. What remains to be seen is how committed the creators will be to fully open access to all the content - if it's truly shared by the whole world as they seem to be saying it will, then it will be a great resource.

the Tamiflu scam

I read today that Tamiflu - the drug that supposedly helps get you better when you have the flu - is now available in ample supply, so Roche doesn't need to make any more. What a scam this is, all taking advantage of public hysteria over the "bird flu" threat (more precisely, the highly pathogenic H5N1 strain of avian influenza virus). Roche advertises Tamiflu on its own website as for both flu prevention and treatment - first of all, there is no evidence I know of that Tamiflu will prevent the flu. If you want to avoid it, get the flu shot, which is a vaccine, and is usually quite effective. Second, the best result you can get with Tamiflu is by taking it right after you get sick, and even then it just shortens the duration of flu symptoms by 1 or 2 days. Not very effective, right? By the time you have the flu, you're usually way too sick to go to your doctor and get a prescription - and you shouldn't even do that, because if you do you're likely to infect others. And finally, we don't have any good evidence that Tamiflu works at all against avian flu.

Meanwhile, though, Roche has got governments (including our own) stockpiling the stuff! And the government officials in charge proudly point to their efforts as if they were doing something about bird flu. What nonsense. If they really want to do something, we need to invest in - and approve - a better, more rapid way to make the vaccine. Right now we make it by growing the virus in chicken eggs - a 50-year-old method that is far too slow and wasteful. We could grow it in cell culture much more quickly and more flexibly (they already do this in Europe), but no company seems interested in trying to get a new method through the laborious FDA approval process. The US gov't ought to just fund this directly, and stop paying for stockpiles of Tamiflu.

UPDATE: Today (May 1) I read this headline: "Roche questions world´s flu pandemic readiness". Turns out that Roche is criticizing the WHO for failing to buy even more Tamiflu! Unbelievable. The spokesman for Roche said, in a press release, "... we believe there is still a long way to terms of meeting treatment preparedness...that could dramatically reduce death rates." This is absurd - Tamiflu doesn't reduce death rates - there is no evidence at all of that - and furthermore, they don't even have evidence that it is particularly effective against avian flu. They're just trying to hype their product and increase sales by scaring people. This is the worst sort of corporate greed. The WHO already has 30 million capsules, and Roche says that governments have ordered an astounding 2.15 billion capsules, all because of fear of bird flu - but this profit windfall isn't enough for them. Their behavior is disgraceful.

the Human Microbiome Project

I spent Sunday evening and all day Monday at a workshop at NIH on the Human Microbiome Project - a new project, not started yet but probably going to start soon. The idea is to sequence the bacteria and other microbes (viruses and even small eukaryotes) that live on our bodies. We have these bugs all over us - in fact, as one of the scientists at the meeting reported, there are probably 10 to 100 times as many microbial cells on/in an average human as there are human cells! Don't worry, the human cells are much, much bigger, so by weight we're still mostly human.

But the point is that we don't really have much idea of what these bugs are that are hitching a ride on us. Some initial DNA sequencing projects - one of which I was involved in, sequencing DNA from the human gut - have found that there are thousands of species, and that the bacterial micro-environments are dramatically different in different areas of our bodies. The mouth has its own microbial environment, for example, which is very different from the skin. But there are big similarities between people - so if you look at the bacteria living in the gut of two different people, they have a lot in common.

It might turn out that many of these bacteria are "inherited" in a Lamarckian sense - that they are passed on from parents at some point during childhood, or maybe even acquired from others in our community. We need to do much more work to find out, and that's what the HMP will be about.

The workshop had some excellent talks by scientists who have taken an early lead in these investigations - Jeff Gordon from U. Indiana, David Relman from Stanford - as well as discussions from Francis Collins of NHGRI about how this fits into their sequencing program. It's clear we have an enormous amount to learn about the bugs on our bodies, and it's very likely that these bugs will turn out to have some interesting connections to our health - so I'm guessing that NIH will fund this in a fairly big way. Stay tuned.

By the way, my friend Jonathan Eisen blogged on this too.

chimps more diverse than humans?

I heard on the news yesterday that a new study discovered that chimps are "more evolved" than humans. It's too bad that the public will get that message, because it is really misleading. What the study found, by studying the genomes of several chimp populations, is that chimps have slightly more genes that appear to be evolving rapidly in response to their environment (this is called "positive selection"). In other words, this one study - whose methods are somewhat inaccurate to begin with, and which can only look at the parts of the genome that encode proteins - found about 225 genes in chimps that are evolving rapidly versus about 150 or so in humans. No surprise there - humans went through a population "bottleneck" in our relatively recent past, long after we diverged from chimps. A bottleneck occurs when the population gets very small, or when only a small number of individuals end up passing on their genes (which has the same effect) to subsequent generations. Anyway, the method didn't even attempt to look at the "noncoding" DNA, which is about 99% of our genome - it only looked at exons. So the study seems to be mostly an attempt to grab a headline, not much more.
But what the heck are we supposed to think a journalist means by "more evolved", anyway? I think the implication is that somehow they are superior to us, and in some ways they are - better at climbing trees, for example! - but this phrase is almost meaningless. Bacteria are "more evolved" too, if you think about it.
The study appeared in the Proceedings of the National Academy of Sciences, which makes the text freely available - so at least it's open access.

Free software and Richard Stallman

So Richard Stallman was in my office last week, and we talked about - what else? - free software. Stallman is famous as the founder of the Free Software Foundation, and perhaps even more famous as the inventor of the GNU software that forms the basis of most of our Unix systems. (He also wrote emacs, my favorite text editor.)
Well, he's quite a character. First of all, don't use the words "open source", "intellectual property," or even "Linux" in his presence, not if you want to finish a sentence. He'll interrupt you to tell you that software must be "free", and no other word will do, and that "intellectual property" is a muddy term that conflates copyrights and patents, and that "Linux" should be "GNU plus Linux" because of all the GNU software that comes wrapped in Linux distributions. I enjoyed talking to him because I agree that software should be free, but he is incredibly dogmatic about it. I don't know if he convinces people who don't already agree with him, but at least he's very up front about his agenda.
He gave a talk in my department (U. Maryland Computer Science) afterwards, and if you're interested, his talks are on his own website.

Free the data

I've been working on the flu virus for several years now, and some of us have been trying hard to get the flu community to share data, but it's an uphill battle. We started a project in 2003 (when I was at TIGR) to sequencing 1000's of influenza genomes and release all the data immediately - so that the entire scientific community can benefit. We've done that, and we've published letters in Nature urging others to do the same, but most of the leading scientists still refuse. They prefer to sit on their data and milk it for whatever results they can discover until all their papers are published, and only then will they release data.
Meanwhile the flu continues to spread around the world and we aren't really keeping ahead of it. Genome data - human, bacterial, viral, whatever - should be released immediately to have the greatest benefit. Any public funding agencies should insist that work funded by them include data release.
I have similar opinions about making our publications free, and I'll try to put some of them in my next post.