Today is the launch of a new type of online publication, a cross between website and a "real" journal, called PLoS Currents: Influenza. What is it? Well, it's a website for immediate publication of new findings about the influenza virus. Submissions are screened by a panel of moderators (I'm one of them) and if they are appropriate, we will publish them immediately - no delays - and they will be freely available for anyone to read. They will also be given a permanent, searching PubMed identification, just like a regular journal paper.
What's the difference between this and a regular journal? Well, first of all, submissions won't be thoroughly reviewed, which means they don't "count" as journal papers, but it also means you can publish them later in a peer-reviewed journal. The Public Library of Science has already bought into this model - they're sponsoring PLoS Currents, after all - and we expect other journals to do so also. So why publish, you might ask? That's easy: in a highly competitive field such as influenza research, different scientists are often racing to answer the same question. By publishing super-rapidly in PLoS Currents, you will get a citable, time-stamped reference that establishes your discovery, and most importantly, establishes when you made it.
The big win here, we hope, is that scientists will be empowered to announce their results to the world without worrying about being "scooped" - a common fear that leads to many results being kept secret for months while papers are prepared and revised. This in turn will speed up scientific progress overall, which is the real goal behind PLoS Currents.
Also, because we aren't looking for complete manuscripts (although those are fine too), we'll accept new observations, new data, and more speculative ideas (as long as they have some data to support them) in PLoS Currents.
We're also pioneering a new way to author papers, using the Google Knol software. After writing your contribution in Google Knol, submission will require little more than a few mouse clicks. To launch the journal, four of its moderators (with colleagues) have posted the first few contributions just these week. Check it out here.
If PLoS Currents: Influenza is successful, it will open the door to an almost unlimited set of new publications in virtually any scientific field. We chose influenza because, with the recent emergence of the new H1N1(A) pandemic flu strain, it became clear to many of us that waiting the typical 3-4 months (at best) for results to appear was just too slow. Similar delays occur in virtually every other area of biomedical research, and it's time we took fuller advantage of the web to speed things up.
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This is Steven Salzberg's blog on science, pseudoscience, medicine, and other topics. I blogged for Forbes for 14 years, but they started censoring me, so I left in October 2024. I'm just here now, uncensored.
Bad medicine at M.D. Anderson Cancer Center
M.D. Anderson Cancer Center (at the University of Texas) is one of the top cancer treatment centers in the United States, and probably in the world. This makes it especially disheartening to see that they have a new website, Cancerwise, that endorses pseudoscientific treatments; in other words, it promotes bad medicine. From what I can see, most of the site discusses perfectly reasonable topics, which makes their endorsement of “woo” especially insidious – how is a patient, or even a scientist from another discipline, supposed to distinguish the real science from the quackery?
What caught my notice in particular – although this is not the only example – is the article “The 3 Most Common Questions People Ask About Acupuncture” written by Lorenzo Cohen. As I and many others have pointed out in previous blog posts, and as the scientific literature shows quite clearly now, acupuncture does not work. When compared to placebo in published trials, the benefits of ‘sham’ acupuncture, where the needles don’t even pierce the skin, are the same as those for ‘real’ acupuncture. Likewise, when the needles are inserted in random positions instead of the ‘real’ acupuncture points, the effects are indistinguishable. So it doesn’t matter where you place the needles, and it doesn’t matter if they pierce the skin – in other words, the only effect is the placebo effect: if a patient believes in acupuncture, and he/she thinks he/she is getting treatment, then they report a mild, subjective improvement in certain types of pain.
With that in mind, here is a disturbing bit of pseudoscience from Cohen’s article:
Cohen also throws in this canard, a quote from his own “integrative medicine” director: “"Can't hurt, might help, why not!" Here’s why: there are real risks to acupuncture, such as infection, and the scientific evidence says the benefit is zero. So here’s my reply: can’t help, might hurt, why do it?
Then, in the section titled “What should I use acupuncture for?”, Cohen writes:
There are other articles promoting pseudoscientific methods on the Cancerwise site, including this one, which applauds Sen. Tom Harkin for his support of NCCAM (which I’ve written about multiple times) and alternative/integrative medicine. I’m sure we’ll see more such articles there, and it’s very dismaying to see woo-meisters like Lorenzo Cohen make progress in their attempts to drag us back into the past, when medicine was little more than guesswork and superstition.
One of our jobs in academia is to be especially critical of ourselves, so when we see an academic center making mistakes, we call them out on it. So I’m joining other bloggers in doing so – notably Orac, who wrote about this same topic last week. (I highly recommend Orac’s lengthy discussion – he thoroughly dismantles Cohen’s claims, including Cohen’s references to studies that supposedly support those claims.) I don’t know who at M.D. Anderson is responsible for the Cancerwise site, but they have a list of 18 authors on that page, and I hope that at least some of them will be concerned to know that they are endorsing pseudoscience.
Here's an idea for another article at Cancerwise: the title can be identical to one of Cohen's section headings: "What should I use acupuncture for?" And the article can be very short, just one word: nothing.
What caught my notice in particular – although this is not the only example – is the article “The 3 Most Common Questions People Ask About Acupuncture” written by Lorenzo Cohen. As I and many others have pointed out in previous blog posts, and as the scientific literature shows quite clearly now, acupuncture does not work. When compared to placebo in published trials, the benefits of ‘sham’ acupuncture, where the needles don’t even pierce the skin, are the same as those for ‘real’ acupuncture. Likewise, when the needles are inserted in random positions instead of the ‘real’ acupuncture points, the effects are indistinguishable. So it doesn’t matter where you place the needles, and it doesn’t matter if they pierce the skin – in other words, the only effect is the placebo effect: if a patient believes in acupuncture, and he/she thinks he/she is getting treatment, then they report a mild, subjective improvement in certain types of pain.
With that in mind, here is a disturbing bit of pseudoscience from Cohen’s article:
“The effects of acupuncture also tend to be cumulative, so it's important not to expect too much too soon. At M. D. Anderson, we consider 8-10 treatments as one course, and for long-term problems, multiple courses may be necessary. I often tell patients with chronic conditions, ‘It's like fertilizing your garden -- don't expect the flowers to bloom tomorrow. In the long-term, though, you should end up with a better result.’ "This is complete nonsense - there is no scientific data to support it. But what is a patient supposed to think when he/she reads that M.D. Anderson recommends 8-10 acupuncture treatments for their patients?
Cohen also throws in this canard, a quote from his own “integrative medicine” director: “"Can't hurt, might help, why not!" Here’s why: there are real risks to acupuncture, such as infection, and the scientific evidence says the benefit is zero. So here’s my reply: can’t help, might hurt, why do it?
Then, in the section titled “What should I use acupuncture for?”, Cohen writes:
“...it's always a good idea to recommend acupuncture when the patient is:Always? Always? How about “never”? There isn’t a single well-done clinical trial demonstrating the effectiveness of acupuncture for any of these conditions. (For a summary of some of the evidence showing its ineffectiveness, see this link at Science-Based Medicine.) Other scientists at M.D. Anderson (are they even paying attention?) should step in and do something to make it clear that the institution doesn’t recommend pseudoscientific, unproven therapies for anything.
* Experiencing uncontrolled nausea, vomiting or pain.
* Experiencing side effects from treatment or medications.
* Has failed conventional treatment for symptom control.”
There are other articles promoting pseudoscientific methods on the Cancerwise site, including this one, which applauds Sen. Tom Harkin for his support of NCCAM (which I’ve written about multiple times) and alternative/integrative medicine. I’m sure we’ll see more such articles there, and it’s very dismaying to see woo-meisters like Lorenzo Cohen make progress in their attempts to drag us back into the past, when medicine was little more than guesswork and superstition.
One of our jobs in academia is to be especially critical of ourselves, so when we see an academic center making mistakes, we call them out on it. So I’m joining other bloggers in doing so – notably Orac, who wrote about this same topic last week. (I highly recommend Orac’s lengthy discussion – he thoroughly dismantles Cohen’s claims, including Cohen’s references to studies that supposedly support those claims.) I don’t know who at M.D. Anderson is responsible for the Cancerwise site, but they have a list of 18 authors on that page, and I hope that at least some of them will be concerned to know that they are endorsing pseudoscience.
Here's an idea for another article at Cancerwise: the title can be identical to one of Cohen's section headings: "What should I use acupuncture for?" And the article can be very short, just one word: nothing.
It’s the 2009 Mexican flu - or is it S-OIV H1N1(A)?
Millions of people have already been infected by the new pandemic influenza virus, and the number may well climb over a billion. The CDC recently estimated that up to 40% of U.S. citizens may be infected over the next year, a startlingly high number. Close to home (for me), several children in my neighborhood came down with influenza just last week. They all recovered, fairly quickly. They almost certainly had the new H1N1 pandemic strain, which seems to be spreading rapidly despite the fact that flu season is normally in the winter. A postdoc in my lab was the first person I know who caught the new pandemic flu – he came down with it in early May, and was very sick for a week. (He stayed home, and no one else was infected, as far as I know.)
But the media are still calling this “swine flu”, in headlines all over the world. Government authorities decided early on to call it 2009 H1N1(A), a catchy name if there ever was one. In one of the earliest scientific publications, CDC scientists called it S-OIV, for “swine-origin influenza virus”.
Nice try, but the media aren't buying it. The problem with the name "swine flu" is that it’s not a swine flu any more. Once an influenza virus has become established in humans, it’s a human flu. If you catch the “swine flu”, you’ll get it from another human – not from a pig. So what to call it?
The choice of a name is actually pretty clear: each of the three 20th-century flu pandemics was named after the geographic location where people believed it originated: the 1918 Spanish flu, the 1957 Asian flu, and the 1968 Hong Kong flu. As best we can tell, the new H1N1(A) virus originated in Mexico, and therefore we should call it the 2009 Mexican flu. This will be accurate and consistent with historical precedent.
And by the way, this idea has already been proposed, but the Mexican government objected, so government health authorities, including the WHO, immediately backed down and looked for a more politically acceptable name. Several countries have already started using the term Mexican flu, including Belgium and Israel, as the AP reported yesterday – although the English-speaking world is still using “swine flu.”
As a side note, we now know that the Spanish flu should have been called “American flu” or possibly “Kansas flu” (where it really started), but during World War I, the U.S. didn’t want to admit that it had a serious health crisis, nor did any of the European countries involved in WWI. The Spanish got stuck with the name – incorrectly – because they didn’t try to hide the fact that they had a pandemic on their hands.
So a note to headline writers in the media: I don’t blame you for calling it swine flu and ignoring alternative names such as S-OIV and H1N1(A). But it’s misleading to use the term “swine flu”, which is already used to refer to influenza viruses circulating among pigs. Calling it “swine flu” also led to the foolish decision by some countries to slaughter large numbers of pigs, which was completely ineffective at controlling the spread of the new virus.
It’s a human flu, and it started in Mexico, so let’s call it Mexican flu.
But the media are still calling this “swine flu”, in headlines all over the world. Government authorities decided early on to call it 2009 H1N1(A), a catchy name if there ever was one. In one of the earliest scientific publications, CDC scientists called it S-OIV, for “swine-origin influenza virus”.
Nice try, but the media aren't buying it. The problem with the name "swine flu" is that it’s not a swine flu any more. Once an influenza virus has become established in humans, it’s a human flu. If you catch the “swine flu”, you’ll get it from another human – not from a pig. So what to call it?
The choice of a name is actually pretty clear: each of the three 20th-century flu pandemics was named after the geographic location where people believed it originated: the 1918 Spanish flu, the 1957 Asian flu, and the 1968 Hong Kong flu. As best we can tell, the new H1N1(A) virus originated in Mexico, and therefore we should call it the 2009 Mexican flu. This will be accurate and consistent with historical precedent.
And by the way, this idea has already been proposed, but the Mexican government objected, so government health authorities, including the WHO, immediately backed down and looked for a more politically acceptable name. Several countries have already started using the term Mexican flu, including Belgium and Israel, as the AP reported yesterday – although the English-speaking world is still using “swine flu.”
As a side note, we now know that the Spanish flu should have been called “American flu” or possibly “Kansas flu” (where it really started), but during World War I, the U.S. didn’t want to admit that it had a serious health crisis, nor did any of the European countries involved in WWI. The Spanish got stuck with the name – incorrectly – because they didn’t try to hide the fact that they had a pandemic on their hands.
So a note to headline writers in the media: I don’t blame you for calling it swine flu and ignoring alternative names such as S-OIV and H1N1(A). But it’s misleading to use the term “swine flu”, which is already used to refer to influenza viruses circulating among pigs. Calling it “swine flu” also led to the foolish decision by some countries to slaughter large numbers of pigs, which was completely ineffective at controlling the spread of the new virus.
It’s a human flu, and it started in Mexico, so let’s call it Mexican flu.
Stimulus funds for pseudoscience
The stimulus funds that the U.S. Congress recently gave to NIH will include $31 million in additional funding for NCCAM, the National Center for Complementary and Alternative Medicine. This is in addition to the $125 million they already had in the current year’s budget. Great. If we spent those funds digging holes and filling them in again, at least a few people might get some exercise, which would benefit their health. That would be a better use than giving the money to NCCAM. Why? Because funding bad science is worse – in many ways – than not funding anything at all. NCCAM continues to provide a home for all sorts of pseudoscience, quackery, and practices that are really no different from voodoo or witchcraft. Allowing NCCAM to operate out of NIH not only gives it an unearned veneer of respectability, it also damages the reputation of NIH. I hate to see this, because NIH is the crown jewel of our biomedical research system.
Let’s look at what NCCAM features on its home page right now. It features the headline “Take charge of your health” followed by six topics. A visitor to the site would have every reason to expect to find sound, science-based advice that would benefit your health under each of these topics. Alas, this is not the case. The first topic is acupuncture, so let’s look at what NCCAM says about it.
The NCCAM accupuncture page is, frankly, an embarrassment. It is one long apologia for acupuncture, dancing around the facts while trying not to admit that the evidence for acupuncture is nonexistent. Indeed, it appears that the authors of the page know that acupuncture doesn’t work, and are trying, in a tortured way, to avoid admitting the truth. The NCCAM's “Key points” on acupuncture are:
Ah, but you might have heard that acupuncture does help to control some types of pain – that’s what its proponents argue. NCCAM has a lengthy page devoted to this topic. What are the key points here? Let’s look:
Recent studies have shown that “sham” acupuncture, where the needles are inserted in random locations, works just as well as “real” acupuncture. Furthermore, it doesn’t even matter if the needles pierce the skin! The patients get the same benefit as long as they think the needles went in. See a longer discussion of this at Science-Based Medicine, where Steven Novella describes one recent trial on acupuncture for back pain – exactly what the NCCAM site claims it works for. Novella expresses the results eloquently:
But wait, I’m not done. Recently, NCCAM proudly announced two new members of its Advisory Council. One of them, Xiaoming Tian, is an acupuncturist. (By Congressional mandate, a majority of the NCCAM board must be selected from proponents of “CAM”. Hmm, voodoo is an "alternative" medicine - I hope they included a voodoo-ist.) So who is this new advisor? His bio says that he is Director of the Academy of Acupuncture and Chinese Medicine at Wildwood Acupuncture Center in Bethesda, Maryland. It’s hard to find much about this school, or Mr. Tian, except from his bio on the website where it says he “has been practicing acupuncture and Chinese herbal medicine in Bethesda, Maryland since 1986” and he is “considered one of the leading researchers in acupuncture and Chinese herbal medicine.” However, he doesn’t seem to have any serious credibility as a researcher: I could locate only one study on which he appears as the second author. And in that study (R.E. Harris et al. The Journal of Alternative and Complementary Medicine. August 2005, 11(4): 663-671) the authors used acupuncture and sham acupuncture to treat fibromyalgia, and found no difference between the “real” and sham versions. That’s because all acupuncture is a sham.
NCCAM is worse than a waste of money. By allowing it to operate within NIH, Congress is giving a false veneer of respect to all sorts of bogus treatments that range from worthless to harmful. To those who argue that some of its funding goes to useful research: if a treatment is promising and scientifically sound, it can be funded by the existing NIH institutes and centers – it doesn’t need the special “free pass” for low-quality research that NCCAM offers. Let's find a better use for that $156 million that NCCAM is getting this year.
Let’s look at what NCCAM features on its home page right now. It features the headline “Take charge of your health” followed by six topics. A visitor to the site would have every reason to expect to find sound, science-based advice that would benefit your health under each of these topics. Alas, this is not the case. The first topic is acupuncture, so let’s look at what NCCAM says about it.
The NCCAM accupuncture page is, frankly, an embarrassment. It is one long apologia for acupuncture, dancing around the facts while trying not to admit that the evidence for acupuncture is nonexistent. Indeed, it appears that the authors of the page know that acupuncture doesn’t work, and are trying, in a tortured way, to avoid admitting the truth. The NCCAM's “Key points” on acupuncture are:
“(1) Acupuncture has been practiced in China and other Asian countries for thousands of years. (2) Scientists are studying the efficacy of acupuncture for a wide range of conditions. (3) Relatively few complications have been reported from the use of acupuncture. However, acupuncture can cause potentially serious side effects if not delivered properly by a qualified practitioner. (4) Tell your health care providers about any complementary and alternative practices you use.“Interesting – the key points don’t include any specific benefits! That’s because every study done has shown that acupuncture doesn’t work any better than placebo, and of course placebo treatments don’t require sticking needles in your body. Let’s look at those key points more closely: the first one is merely an “argument from authority” – i.e., people have been doing this for a long time, and we are supposed to infer that therefore it works. Hardly! If we used the same medical practices that were used in China thousands of years ago, we’d have the same life expectancy – perhaps 30-40 years. Not good. Point 2 just states that studies are under way (funded by NCCAM, I might add), but doesn’t point out that all the studies are negative! The third point just says that you probably won’t be injured by acupuncture (but you never know). So it seems that the NCCAM folks know that science doesn’t support any benefit from the use of acupuncture, but they can’t just say that on their website – why? Because NCCAM’s staff view its mission (apparently) as the promotion of “alternatives” to medicine, even if those alternatives are nonsense.
Ah, but you might have heard that acupuncture does help to control some types of pain – that’s what its proponents argue. NCCAM has a lengthy page devoted to this topic. What are the key points here? Let’s look:
“(1) People use acupuncture for various types of pain. Back pain is the most commonly reported use, followed by joint pain, neck pain, and headache. (2) Acupuncture is being studied for its efficacy in alleviating many kinds of pain. There are promising findings in some conditions, such as chronic low-back pain and osteoarthritis of the knee; but, for most other conditions, additional research is needed. The National Center for Complementary and Alternative Medicine (NCCAM) sponsors a wide range of acupuncture research. (3) Acupuncture is generally considered safe when performed correctly. (4) In traditional Chinese medicine theory, acupuncture regulates the flow of qi (vital energy) through the body. Research to test scientific theories about how acupuncture might work to relieve pain is under way.”These points are a pathetic attempt to apologize for acupuncture, without admitting that it doesn’t work. First they say that lots of people use it – true enough, but are we supposed to believe that means it works? In that case, why do any science at all? Why not just look at what people are doing, and follow their lead? Then they say that acupuncture is being studied by NCCAM, and they claim “promising” results in some conditions. But “additional research is needed” for others. Sorry, NCCAM, but more research is not needed – multiple studies have shown that acupuncture doesn’t work. If it weren’t for lobbying efforts by acupuncturists and their ilk, who have a major financial interest in seeing these studies continue, this topic would be dead. And point (4) about qi is just embarrassing. There's never been any evidence that qi exists, and NIH/NCCAM should not even mention it.
Recent studies have shown that “sham” acupuncture, where the needles are inserted in random locations, works just as well as “real” acupuncture. Furthermore, it doesn’t even matter if the needles pierce the skin! The patients get the same benefit as long as they think the needles went in. See a longer discussion of this at Science-Based Medicine, where Steven Novella describes one recent trial on acupuncture for back pain – exactly what the NCCAM site claims it works for. Novella expresses the results eloquently:
“Imagine if we were evaluating the efficacy of a new pain drug. This drug, when tested in open trials (no blinding or control) has an effect on reducing pain - it is superior to no treatment. When compared to a placebo, however, the drug is no more effective than the placebo, although both are more effective than no treatment.Despite the claims at the NCCAM site, acupuncture has not been shown effective for any type of pain, and it does have potential side effects – infection from improperly sterilized needles, for example. Why risk infection for a treatment with no benefit?
Now imagine that the pharmaceutical company who manufactures this drug sends out a press release declaring that their drug is effective for pain, but that their research shows that a placebo of their drug is also effective (FDA applications are pending). Therefore more research is needed to determine how their drug works. Would you buy it?
That is the exact situation we are facing with acupuncture research.”
But wait, I’m not done. Recently, NCCAM proudly announced two new members of its Advisory Council. One of them, Xiaoming Tian, is an acupuncturist. (By Congressional mandate, a majority of the NCCAM board must be selected from proponents of “CAM”. Hmm, voodoo is an "alternative" medicine - I hope they included a voodoo-ist.) So who is this new advisor? His bio says that he is Director of the Academy of Acupuncture and Chinese Medicine at Wildwood Acupuncture Center in Bethesda, Maryland. It’s hard to find much about this school, or Mr. Tian, except from his bio on the website where it says he “has been practicing acupuncture and Chinese herbal medicine in Bethesda, Maryland since 1986” and he is “considered one of the leading researchers in acupuncture and Chinese herbal medicine.” However, he doesn’t seem to have any serious credibility as a researcher: I could locate only one study on which he appears as the second author. And in that study (R.E. Harris et al. The Journal of Alternative and Complementary Medicine. August 2005, 11(4): 663-671) the authors used acupuncture and sham acupuncture to treat fibromyalgia, and found no difference between the “real” and sham versions. That’s because all acupuncture is a sham.
NCCAM is worse than a waste of money. By allowing it to operate within NIH, Congress is giving a false veneer of respect to all sorts of bogus treatments that range from worthless to harmful. To those who argue that some of its funding goes to useful research: if a treatment is promising and scientifically sound, it can be funded by the existing NIH institutes and centers – it doesn’t need the special “free pass” for low-quality research that NCCAM offers. Let's find a better use for that $156 million that NCCAM is getting this year.
Dinosaur proteins from T. rex and hadrosaurs
The controversy over the finding of Tyrannosaurus rex proteins in a fossilized bone
continues, with a long article in Wired magazine this week exploring the issue. The Wired reporter, Evan Ratliff, takes a refreshingly skeptical view through much of the article. It's a good read, and I recommend it.
But first, an update on the science: Mary Schweitzer, John Asara and colleagues published a new report in Science on May 1 describing their analysis of an 80-million-year-old fossil from the dinosaur Brachylophosaurus canadensis, a hadrosaur that is 12 million years older than T. rex. Once again, they found fragments from collagen, the protein that is a major component of bone, and as with their original T. rex study, they claim that these represent original dinosaur proteins. And as before, they found that the dinosaur proteins most closely resemble modern birds – in particular, ostrich.
The new study spends a significant amount of effort addressing the question of contamination. This question has been raised in at least two ways. Tom Kaye and colleagues reported in PLoS ONE that the soft tissue found by Schweitzer could be explained as a bacterial biofilm, rather than as preserved dinosaur tissue. I still like the biofilm explanation, and I don’t see how the new study refutes it. The study contains many microscope photos showing how the fine structure of the fossilized bone resembles modern ostrich bone, but preserved physical structure is not in question. The real question is, did dinosaur proteins survive for 80 million years in these bones?
The second contamination question emerges from this: Marty McIntosh discovered – after Asara released his mass spec data to the public – that the original T. rex sample contained hemoglobin. This finding has been discussed in the mass spec community, and privately among a group of scientists (including me) following this story, but it has not been published (as far as I know) until the Wired article.
Hemoglobin! Now, from what I know, we don’t expect to find much hemoglobin in bone tissue, and we sure don’t expect to find it in 68-million-year-old fossils. Could this be another big discovery? Or could it, perhaps, be that the sample is contaminated with modern proteins, perhaps from ostrich?
Upon further inquiry, a number of scientists learned that John Asara’s lab had indeed used its mass spec equipment to analyze samples of ostrich bone. Asara reports (in the Wired article) that the ostrich sample had been analyzed long before either of the dinosaurs:
If the T. rex sample was contaminated, that throws all the results into question. It also throws into question the new hadrosaur results – if contamination was a problem before, it might be still. The best way to resolve this is for an independent group to take the original fossils and repeat the study. I know that there are groups trying to do exactly this, but the fossils are controlled by paleontologist Jack Horner, who thus far has refused to share them with anyone but Schweitzer.
Extraordinary claims require extraordinary evidence, as any good skeptic knows. The finding of intact collagen protein in dinosaur fossils is certainly an extraordinary claim, and the finding of hemoglobin is even more stunning. Alas, the alternative explanations (statistical artifacts - see my earlier blogs and Pavel Pevzner's article in Science - and contamination by bacteria and/or ostrich tissue) are much more likely. I'd love for these results to be true - intact dinosaur proteins! Think of all the evolutionary comparisons we could do if we can reconstruct the past 80 million years directly from the molecular record! But I'm afraid I remain skeptical.
continues, with a long article in Wired magazine this week exploring the issue. The Wired reporter, Evan Ratliff, takes a refreshingly skeptical view through much of the article. It's a good read, and I recommend it.
But first, an update on the science: Mary Schweitzer, John Asara and colleagues published a new report in Science on May 1 describing their analysis of an 80-million-year-old fossil from the dinosaur Brachylophosaurus canadensis, a hadrosaur that is 12 million years older than T. rex. Once again, they found fragments from collagen, the protein that is a major component of bone, and as with their original T. rex study, they claim that these represent original dinosaur proteins. And as before, they found that the dinosaur proteins most closely resemble modern birds – in particular, ostrich.
The new study spends a significant amount of effort addressing the question of contamination. This question has been raised in at least two ways. Tom Kaye and colleagues reported in PLoS ONE that the soft tissue found by Schweitzer could be explained as a bacterial biofilm, rather than as preserved dinosaur tissue. I still like the biofilm explanation, and I don’t see how the new study refutes it. The study contains many microscope photos showing how the fine structure of the fossilized bone resembles modern ostrich bone, but preserved physical structure is not in question. The real question is, did dinosaur proteins survive for 80 million years in these bones?
The second contamination question emerges from this: Marty McIntosh discovered – after Asara released his mass spec data to the public – that the original T. rex sample contained hemoglobin. This finding has been discussed in the mass spec community, and privately among a group of scientists (including me) following this story, but it has not been published (as far as I know) until the Wired article.
Hemoglobin! Now, from what I know, we don’t expect to find much hemoglobin in bone tissue, and we sure don’t expect to find it in 68-million-year-old fossils. Could this be another big discovery? Or could it, perhaps, be that the sample is contaminated with modern proteins, perhaps from ostrich?
Upon further inquiry, a number of scientists learned that John Asara’s lab had indeed used its mass spec equipment to analyze samples of ostrich bone. Asara reports (in the Wired article) that the ostrich sample had been analyzed long before either of the dinosaurs:
“Asara conducted his ostrich and T. rex experiments a year and a half apart, separated by roughly 1,500 mass spectrometry runs. According to Asara, none of those spectra, nor samples of the soil surrounding the fossils, nor his daily control runs—in which he sequences known solutions to check for contaminants—turned up any ostrich hemoglobin.”The new Science paper on the hadrosaur proteins doesn’t mention the (unpublished) hemoglobin fragments in the T. rex data, so this important question was not addressed. Well, if Asara’s lab handled ostrich material, then I remain skeptical of their assurances that ostrich couldn’t have possibly contaminated the original T. rex samples. And Marty McIntosh explained to the Wired reporter that “a chemical modification on the hemoglobin makes it more likely to be contamination.” McIntosh submitted a paper on his results to Science, but they rejected it – perhaps because it called into a question a finding that Science’s editors have obviously endorsed. That’s too bad.
If the T. rex sample was contaminated, that throws all the results into question. It also throws into question the new hadrosaur results – if contamination was a problem before, it might be still. The best way to resolve this is for an independent group to take the original fossils and repeat the study. I know that there are groups trying to do exactly this, but the fossils are controlled by paleontologist Jack Horner, who thus far has refused to share them with anyone but Schweitzer.
Extraordinary claims require extraordinary evidence, as any good skeptic knows. The finding of intact collagen protein in dinosaur fossils is certainly an extraordinary claim, and the finding of hemoglobin is even more stunning. Alas, the alternative explanations (statistical artifacts - see my earlier blogs and Pavel Pevzner's article in Science - and contamination by bacteria and/or ostrich tissue) are much more likely. I'd love for these results to be true - intact dinosaur proteins! Think of all the evolutionary comparisons we could do if we can reconstruct the past 80 million years directly from the molecular record! But I'm afraid I remain skeptical.
Alt meds for pets? Really?
The Washington Post has had two articles this week on "alternative" treatments, both of them very poorly researched, both written by reporters who just couldn't gush enough over the possibilities for cures promised by promoters of treatments such as Reiki, homeopathy, acupuncture, and Chinese herbs. It's too painful for me to repeat the claims of the first article - which was little more than marketing hype, focusing on a physician who was offering these treatments to her human patients - so I'll just mention today's article, which is titled "Going Beyond the Usual Rx for Rover: Alternative Treatments Gaining Acceptance."
According to the article, veterinarians who believe (despite the complete lack of evidence) "that such alternative therapies as acupuncture and Chinese herbs can help animals struggling with arthritis and allergies are finding growing acceptance from some peers and an eager reception from pet owners." The article quotes several veterinarians (is it really accurate to call them vets? I wonder) in northern Virginia who now specialize in acupuncture and homeopathy for pets.
The evidence for these therapies, when they've been studied properly, is that they offer no benefit other than the placebo effect. For treatment of pain, patients who think they're getting almost any treatment (including acupuncture) tend to report that they are feeling somewhat less pain - even if the treatment is a "sham" treatment such as a sugar pill or sham acupuncture. That's fine for people, but what about pets? You can't explain to Fido why the good doctor is sticking needles into him. Ouch!
These treatments aren't cheap - "alt vets" charge about $100 for an acupuncture session, according to the article. One doctor in Bethesda, Maryland offers ozone therapy to treat cancer and kidney failure. I wonder what that costs? Do these vets know that the American Cancer Foundation strongly advises cancer patients against ozone therapy (yes, it is heavily marketed for people too), noting that "there is no evidence that ozone is effective for the treatment of cancer"?
From the Post article, it's pretty clear that the placebo effect is once again operating, but it's affecting the pet owners, not the pets. Several owners are quoted saying how they saw their pets improve after homeopathy or acupuncture. One dog owner brings her border collie in for an "acupuncture tuneup" (no, I'm not making this up! if only I were so clever) every three months. The owner, who obviously believes this works, reports that "after a session here, she [the collie] runs like a puppy." I would too, after escaping those sharp needles for another three-month reprieve!
According to the article, veterinarians who believe (despite the complete lack of evidence) "that such alternative therapies as acupuncture and Chinese herbs can help animals struggling with arthritis and allergies are finding growing acceptance from some peers and an eager reception from pet owners." The article quotes several veterinarians (is it really accurate to call them vets? I wonder) in northern Virginia who now specialize in acupuncture and homeopathy for pets.
The evidence for these therapies, when they've been studied properly, is that they offer no benefit other than the placebo effect. For treatment of pain, patients who think they're getting almost any treatment (including acupuncture) tend to report that they are feeling somewhat less pain - even if the treatment is a "sham" treatment such as a sugar pill or sham acupuncture. That's fine for people, but what about pets? You can't explain to Fido why the good doctor is sticking needles into him. Ouch!
These treatments aren't cheap - "alt vets" charge about $100 for an acupuncture session, according to the article. One doctor in Bethesda, Maryland offers ozone therapy to treat cancer and kidney failure. I wonder what that costs? Do these vets know that the American Cancer Foundation strongly advises cancer patients against ozone therapy (yes, it is heavily marketed for people too), noting that "there is no evidence that ozone is effective for the treatment of cancer"?
From the Post article, it's pretty clear that the placebo effect is once again operating, but it's affecting the pet owners, not the pets. Several owners are quoted saying how they saw their pets improve after homeopathy or acupuncture. One dog owner brings her border collie in for an "acupuncture tuneup" (no, I'm not making this up! if only I were so clever) every three months. The owner, who obviously believes this works, reports that "after a session here, she [the collie] runs like a puppy." I would too, after escaping those sharp needles for another three-month reprieve!
Frightening quack autism treatment
One of the most bizarre and frightening "treatments" being promoted for autism is a drug, Lupron, which suppresses testosterone. Treatment with Lupron is also known as "chemical castration," and as you can imagine, it's a very serious and potentially harmful drug. But Mark and David Geier have decided - despite the complete lack of evidence for this - that excess testosterone causes autism, and that (therefore) Lupron will cure it.
The Geiers have been promoting this for years, but a recent article in the Chicago Tribune caught my attention. The title of the article is ' "Miracle drug" called junk science', and the Tribune deserves some credit for producing a reasonably skeptical article. "Lupron is the miracle drug," says Mark Geier, who doesn't hesitate to make outrageous claims. Mark Geier has an M.D., although he is not qualified in the specialties (such as pediatic neurology) that he would need to understand autism. His son, David Geier, has only an undergraduate degree in biology. Despite this, they are marketing their "Lupron protocol" around the country, happy to profit from this outrageous, harmful treatment. The Geiers have filed for a patent on their Lupron treatment, and they charge $12,000 to autistic patients for initial diagnostic tests, plus $5000-$6000 per month for the Lupron therapy.
The Tribute article was prompted by an appearance made by the Geiers in the Chicago area, where they were speaking at the Autism One conference. Here is a quote from the Geiers' abstract of their presentation:
As evidence for their Lupron treatment, the Geiers often cite a study they published themselves several years ago, which experts have pointed out is deeply flawed. (Somehow I doubt that they ever point out that some of their published research was subsequently retracted by the journal Autoimmunity Reviews.) The Tribune reporter interviewed Dr. Paul Kaplowitz, chief of endocrinology at Children's National Medical Center in Washington, who pointed out that the Geiers don't seem to understand that the blood tests they used in their study did not show elevated testosterone. Kaplowitz asked, "Is Dr. Geier just misinformed and he hasn't studied endocrinology, or is he trying to mislead?" Admittedly, it's hard to know in cases like these whether the quacks are truly ignorant, or whether they know they're peddling nonsense and just don't care.
Local Chicago-area doctor Mayer Eisenstein, who is making the Lupron protocol available and who supports the Geiers, was also interviewed by the Tribune. Eisenstein has his own pseudoscientific claims, and he too is a featured speaker at the Autism One conference. His speaker abstract states:
By the way, if you want a guide to autism quackery, take a look at the Autism One conference site. But be warned: if you care about science, you might be in for a painful experience. I couldn't take it for long myself.
Also quoted in the Tribune was Dr. Simon Baron-Cohen, a professor of developmental psychopathology director of the Autism Research Center at Cambridge University, who said "The idea of using it [Lupron] with vulnerable children with autism, who do not have a life-threatening disease and pose no danger to anyone, without a careful trial to determine the unwanted side effects or indeed any benefits, fills me with horror." Well said.
What's hard for me to understand is how the medical profession can allow someone like Mark Geier to continue to practice medicine. One of the principals that all medical students are taught, supposedly, is "first, do no harm." Apparently, Mark Geier didn't learn that one.
The Geiers have been promoting this for years, but a recent article in the Chicago Tribune caught my attention. The title of the article is ' "Miracle drug" called junk science', and the Tribune deserves some credit for producing a reasonably skeptical article. "Lupron is the miracle drug," says Mark Geier, who doesn't hesitate to make outrageous claims. Mark Geier has an M.D., although he is not qualified in the specialties (such as pediatic neurology) that he would need to understand autism. His son, David Geier, has only an undergraduate degree in biology. Despite this, they are marketing their "Lupron protocol" around the country, happy to profit from this outrageous, harmful treatment. The Geiers have filed for a patent on their Lupron treatment, and they charge $12,000 to autistic patients for initial diagnostic tests, plus $5000-$6000 per month for the Lupron therapy.
The Tribute article was prompted by an appearance made by the Geiers in the Chicago area, where they were speaking at the Autism One conference. Here is a quote from the Geiers' abstract of their presentation:
"Finally, attendees will be presented newly published peer-reviewed clinical studies on over 200 patients diagnosed with autism showing that interventions designed to lower or significantly reduce the functionality of testosterone (and other androgens) were observed to significant improve clinical outcomes. The new information presented may provide an important alternate treatment course for many patients diagnosed with autism that are presently administered psychiatric medications. "It sounds reasonable - but only if you don't know anything about the Geiers' history, or the profits they are making from their supposed "cure."
As evidence for their Lupron treatment, the Geiers often cite a study they published themselves several years ago, which experts have pointed out is deeply flawed. (Somehow I doubt that they ever point out that some of their published research was subsequently retracted by the journal Autoimmunity Reviews.) The Tribune reporter interviewed Dr. Paul Kaplowitz, chief of endocrinology at Children's National Medical Center in Washington, who pointed out that the Geiers don't seem to understand that the blood tests they used in their study did not show elevated testosterone. Kaplowitz asked, "Is Dr. Geier just misinformed and he hasn't studied endocrinology, or is he trying to mislead?" Admittedly, it's hard to know in cases like these whether the quacks are truly ignorant, or whether they know they're peddling nonsense and just don't care.
Local Chicago-area doctor Mayer Eisenstein, who is making the Lupron protocol available and who supports the Geiers, was also interviewed by the Tribune. Eisenstein has his own pseudoscientific claims, and he too is a featured speaker at the Autism One conference. His speaker abstract states:
"if children do not get polio because of the polio vaccine but later die of a cancer caused by the SV40 virus received as a contaminant in the vaccine, the risk may outweigh the benefits."Ouch. There's no evidence that the polio vaccine causes cancer - none whatsoever. That doesn't seem to be a concern for Eisenstein, whose bio on the Autism One site proudly claims that "he has formulated natural pharmaceuticals which can be used to treat many chronic medical conditions." These are modern snake-oil salesmen. Maybe Eisenstein is really so ignorant that he thinks the polio vaccine was a bad idea, but I think he just doesn't care.
By the way, if you want a guide to autism quackery, take a look at the Autism One conference site. But be warned: if you care about science, you might be in for a painful experience. I couldn't take it for long myself.
Also quoted in the Tribune was Dr. Simon Baron-Cohen, a professor of developmental psychopathology director of the Autism Research Center at Cambridge University, who said "The idea of using it [Lupron] with vulnerable children with autism, who do not have a life-threatening disease and pose no danger to anyone, without a careful trial to determine the unwanted side effects or indeed any benefits, fills me with horror." Well said.
What's hard for me to understand is how the medical profession can allow someone like Mark Geier to continue to practice medicine. One of the principals that all medical students are taught, supposedly, is "first, do no harm." Apparently, Mark Geier didn't learn that one.
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