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?
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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.
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.
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?
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.
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 quackwatch.com. 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.
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 quackwatch.com. 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.
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 www.baskeptics.org: 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.
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.
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