I'm away right now, and haven't had time to prepare new stuff. So, here's something from the archives again: by which I mean, something written in 2006. It's still pretty interesting (in my humble opinion), but I would definitely do some things differently were I to re-write it today [gliding sifaka below from Demes et al. (1991): read on]. Mention 'flying primate' and most zoologists will think you're referring to the well known, controversial theory of John Pettigrew of the University of Queensland. And if that sentence sounds familiar, it's because I used it previously to introduce a post all about Pettigrew's controversial theory that megabats are not close relatives of microbats, but are instead close relatives of us primates. As reviewed in that post, currently the data does not favour the idea that the two bat groups evolved independently, and the 'flying primate' theory has not won widespread acceptance. The term 'flying primate' might be better attached however to another group of mammals, and this time they really are undeniable primates. They are lemurs, and they fly. Well... fly sort of. Read the rest of this post... | Read the comments on this post... Also check out the featured ScienceBlog of the week: Inside the Outbreaks on the ScienceBlogs Book Club

This is interesting: Drupal has released a new code of conduct for their community. It has five points: * Be considerate
* Be respectful
* When we disagree, we consult others
* When we are unsure, we ask for help
* Step down considerately The fucker stole the whole thing from Ubuntu, as it turns out. How dare they!!!!111eleventy!!! Gmail just got like skype, sort of. Five days after the announcement of Voice and Video Chat service in Gmail for Debian-based Linux distributions, Google unveiled a Gmail phone call service for Windows, Mac, and Linux. Rather than having both parties tied to their computers and logged into their Gmail accounts, one user can now call anyone in the US and Canada with telephone service. Google states that rates will remain free for the rest of the year and very low for international calls. source
Aircraft Flight Recorder technology is hardly ever upgraded, and thus, will always be stagnant. Why is that? Why are the designers of something so important so conservative? Maybe they should be. But really, there is no reason that when an airplane crashes, all the flight data has not already been downloaded as part of a continuous process using high speed networks and satellites. That would have been nice for Flight 447, oui? Anyway, here's a story about black box upgrades. Read the comments on this post...

If you teach biology, you probably get to hydrogen bonding pretty early in the term. Here's an inspirational video for you: hat tip: Bora Hydrogen bonding explains everything!!!! Why does water hold so much heat? Why does ice float? How does a water bug not sink? Why does a dog smell everyone's butt? Read the comments on this post...

An offshore oil rig exploded in the Gulf of Mexico on Thursday, west of the site of the April blast that caused the massive oil spill. A commercial helicopter company reported the blast around 9:30 a.m. CDT Thursday, Coast Guard Petty Officer Casey Ranel said. Seven helicopters, two airplanes and four boats were en route to the site, about 80 miles south of Vermilion Bay along the central Louisiana coast. The Coast Guard said initial reports indicated all 13 crew members from the rig were in the water. One was injured, but there were no deaths. details Read the comments on this post...

"Hey, dude, whatcha doin'?" "Signing these contracts. I'm not sure why they need four copies, but they do." "Contracts for what?" "The new book. Remmeber, the one we've been talking about these last few weeks? Sequel-of-sorts to How to Teach Physics to Your Dog? About relativity?" "Oh, yeah, that's right! We're doing another book! Where do I sign?" "What do you mean, 'Where do I sign?' You're a dog." "I could, you know, put a paw print on the line, or something." "I suppose you could, but it wouldn't be legally binding. Dogs aren't allowed to sign contracts." "You know that's horribly species-ist, right? I suppose you're going to get all the money, too." "Well, yeah, since dogs can't open bank accounts, either. But don't worry, you'll get your share." "In the form of steak?" "Absolutely." "Yippee! I love steak!" Read the rest of this post... | Read the comments on this post... Also check out the featured ScienceBlog of the week: Inside the Outbreaks on the ScienceBlogs Book Club

Some good news: the online 'debate' between Dawkins and the religion editors of the Times can be read for free. It's a terrible format: it's just a chat window with people throwing questions at Dawkins, which he deftly slices out of the air with a samurai sword of reason. Here's one of the more coherent questions the pro-faith gummi bears tossed at him, which will give you an idea of the quality of the interrogation. I just interviewed David Wilkinson, principal of St John's Durham and astrophysicist, and this is what he said (full interview at my Times blog Articles of Faith): The science Stephen Hawking uses raises a number of questions which for many opens the door to the possibility of an existence of a creator and for many points to the existence of a creator. 'One would be the the purpose of the universe. Although science might discover the mechanism, we are still left with the question of what is the purpose. 'Second is where the laws of physics come from. Science subsumes the laws but we are still left with the question of where the laws come from. 'Third is the intelligibility of the universe. It strikes me as interesting that Stephen Hawking can make it intelligible. Albert Einstein once said that the most incomprehensible thing about the universe is that it is comprehensible. For many of us who are struck by the intelligibility of the physical laws, the explanation is that the creator is the force of rationality both for the universe and for our minds. To summarize Dawkins' three answers: Why even propose a cosmic purpose? That question isn't answered by postulating a mysterious intelligent being, either. Why assume a godless universe would have to be unintelligible? Stupid questions do not warrant our concern or need to answer. Questions that do not bring us closer to understanding are nothing but the posturings of people who substitute noise for reason. Read the comments on this post...

I lifted this from the fourth in a series on "why we vaccinate" from Elyse the Skepchick's blog. The first one is here. Read the comments on this post...

From the Guardian: Is physicist Stephen Hawking right that physics, not God, created the universe? 81.3% Yes. I believe in gravity, not divinity
18.7% No. God: Hawking 'not necessary' Somebody show me the units of divinity, please, as well as a few measurements that show the goodness of fit to theory. Oh, and show the formula, too. Read the comments on this post...

The dust is starting to settle after the Hauser-gate scandal which rocked psychology a couple of weeks back.

Harvard Professor Marc Hauser has been investigated by a faculty committee and the verdict was released on the 20th August: Hauser was "found solely responsible... for eight instances of scientific misconduct." He's taking a year's "leave", his future uncertain.

Unfortunately, there has been no official news on what exactly the misconduct was, and how much of Hauser's work is suspect. According to Harvard, only three publications were affected: a 2002 paper in Cognition, which has been retracted; a 2007 paper which has been "corrected" (see below), and another 2007 Science paper, which is still under discussion.

But what happened? Cognition editor Gerry Altmann writes that he was given access to some of the Harvard internal investigation. He concludes that Hauser simply invented some of the crucial data in the retracted 2002 paper.

Essentially, some monkeys were supposed to have been tested on two conditions, X and Y, and their responses were videotaped. The difference in the monkey's behaviour between the two conditions was the scientifically interesting outcome.

In fact, the videos of the experiment showed them being tested only on condition X. There was no video evidence that condition Y was even tested. The "data" from condition Y, and by extension the differences, were, apparently, simply made up.

If this is true, it is, in Altmann's words, "the worst form of academic misconduct." As he says, it's not quite a smoking gun: maybe tapes of Y did exist, but they got lost somehow. However, this seems implausible. If so, Hauser would presumably have told Harvard so in his defence. Yet they found him guilty - and Hauser retracted the paper.

So it seems that either Hauser never tested the monkeys on condition B at all, and just made up the data, or he did test them, saw that they weren't behaving the "right" way, deleted the videos... and just made up the data. Either way it's fraud.

Was this a one-off? The Cognition paper is the only one that's been retracted. But another 2007 paper was "replicated", with Hauser & a colleague recently writing:
In the original [2007] study by Hauser et al., we reported videotaped experiments on action perception with free ranging rhesus macaques living on the island of Cayo Santiago, Puerto Rico. It has been discovered that the video records and field notes collected by the researcher who performed the experiments (D. Glynn) are incomplete for two of the conditions.Luckily, Hauser said, when he and a colleague went back to Puerto Rico and repeated the experiment, they found "the exact same pattern of results" as originally reported. Phew.

This note, however, was sent to the journal in July, several weeks before the scandal broke - back when Hauser's reputation was intact. Was this an attempt by Hauser to pin the blame on someone else - David Glynn, who worked as a research assistant in Hauser's lab for three years, and has since left academia?

As I wrote in my previous post:
Glynn was not an author on the only paper which has actually been retracted [the Cognition 2002 paper that Altmann refers to]... according to his resume, he didn't arrive in Hauser's lab until 2005.Glynn cannot possibly have been involved in the retracted 2002 paper. And Harvard's investigation concluded that Hauser was "solely responsible", remember. So we're to believe that Hauser, guilty of misconduct, was himself an innocent victim of some entirely unrelated mischief in 2007 - but that it was all OK in the end, because when Hauser checked the data, it was fine.

Maybe that's what happened. I am not convinced.

Personally, if I were David Glynn, I would want to clear my name. He's left science, but still, a letter to a peer reviewed journal accuses him of having produced "incomplete video records and field notes", which is not a nice thing to say about someone.

Hmm. On August 19th, the Chronicle of Higher Education ran an article about the case, based on a leaked Harvard document. They say that "A copy of the document was provided to The Chronicle by a former research assistant in the lab who has since left psychology."

Hmm. Who could blame them for leaking it? It's worth remembering that it was a research assistant in Hauser's lab who originally blew the whistle on the whole deal, according to the Chronicle.

Apparently, what originally rang alarm bells was that Hauser appeared to be reporting monkey behaviours which had never happened, according to the video evidence. So at least in that case, there were videos, and it was the inconsistency between Hauser's data and the videos that drew attention. This is what makes me suspect that maybe there were videos and field notes in every case, and the "inconvenient" ones were deleted to try to hide the smoking gun. But that's just speculation.

What's clear is that science owes the whistle-blowing research assistant, whoever it is, a huge debt.

Laplace, Hawking, same difference. In a completely unsurprising move, Stephen Hawking has made it clear that we have no need for the god hypothesis. Modern physics leaves no place for God in the creation of the Universe, Stephen Hawking has concluded. Just as Darwinism removed the need for a creator in the sphere of biology, Britain's most eminent scientist argues that a new series of theories have rendered redundant the role of a creator for the Universe. In his forthcoming book, an extract from which is published exclusively in Eureka, published today with The Times, Professor Hawking sets out to answer the question: "Did the Universe need a creator?" The answer he gives is a resounding "no". Far from being a once-in-a-million event that could only be accounted for by extraordinary serendipity or a divine hand, the Big Bang was an inevitable consequence of the laws of physics, Hawking says. "Because there is a law such as gravity, the Universe can and will create itself from nothing. Cue condemnations and histrionics, stage left. Fulminations and denial, stage right. Like it says, this is from an upcoming book, so I haven't read it yet, and The Times seems to have moved everything behind a paywall, so I can't even read the full article or any of the associated content, but the story itself sounds a bit banal. The theists have never offered a single credible, logical reason to incorporate a cosmic intelligence into the history of the universe, and it's about time they were flatly rebuffed and told their contributions are unnecessary. Besides the annoying paywall, though, I have to point out another nasty element of the reporting — they must really hate Richard Dawkins at The Times. When it comes to religion, Stephen Hawking is the voice of reason. Not for him the polemical style that has propelled Richard Dawkins to the fore of national consciousness in the God debates. His argument is likely in the long term to be more dangerous to religion because it is more measured than The God Delusion. The God Delusion was a calm and measured book, and Richard Dawkins' talks are polite, rational events. Have these people even read the book? It looks to me as if they are trying to mollify their readers by setting up a Saint Hawking while reassuring everyone that they can still beat up on Devil Dawkins. Read the comments on this post...

My old friend, colleague, suaboya, and educator extraordinaire, Jay Phelan has written what many believe will be the next Campbell. The name of the book is What Is Life?. There are two versions: one regular, and one with extra physiology. And both are based firmly on and integrated thoroughly with excellent evolutionary biology. Read the rest of this post... | Read the comments on this post...

Nearly a month ago, I expressed my dismay and displeasure at the infiltration fo quackademic medicine into what is arguably the premier medical journal in the world, The New England Journal of Medicine (NEJM) in the form of a highly credulous review on the use of acupuncture for low back pain that brought eternal shame on the hallowed pages of a once-great journal. As Mark Crislip put it, trust, once damaged or lost, is very hard to restore, and I definitely lost a lot of trust for the NEJM compared to what I had for it a month ago. Since then, I've been keeping my eyes out for other examples of quackademic medicine infiltrating various peer-reviewed journals. Unfortunately, I have not lacked for examples. Fresh in my memory, though, remains the stench of quackademic medicine in the NEJM. Unfortunately, just as the faint odor of urine can be revived by hot and humid weather, the stench of quackademic medicine at the NEJM was restored, at least in my memory, by an article that a reader sent to me. Apparently someone was interested in just who some of the writers of the NEJM article were. At the time, when I wrote about the article, I didn't really care too much about any of the authros other than the lead author, Dr. Brian Berman. Apparently this reader thought I should check out at least one of the other authors, which I proceeded to do. I happened to pick Dr. Helene M. Langevin of the University of Vermont. (Who knew Vermont had quackademic medicine?) One thing led to another (PubMed, specifically), and suddenly I found this gem of a quackademic medicine article by Dr. Langevin in, of all places PLoS ONE, entitled Electrical Impedance of Acupuncture Meridians: The Relevance of Subcutaneous Collagenous Bands. Senior author? Dr. Langevin. Funding source? What do you think? The National Center for Complementary and Alternative Medicine (NCCAM), of course! Read the rest of this post... | Read the comments on this post...

Nearly a month ago, I expressed my dismay and displeasure at the infiltration fo quackademic medicine into what is arguably the premier medical journal in the world, The New England Journal of Medicine (NEJM) in the form of a highly credulous review on the use of acupuncture for low back pain that brought eternal shame on the hallowed pages of a once-great journal. As Mark Crislip put it, trust, once damaged or lost, is very hard to restore, and I definitely lost a lot of trust for the NEJM compared to what I had for it a month ago. Since then, I've been keeping my eyes out for other examples of quackademic medicine infiltrating various peer-reviewed journals. Unfortunately, I have not lacked for examples. Fresh in my memory, though, remains the stench of quackademic medicine in the NEJM. Unfortunately, just as the faint odor of urine can be revived by hot and humid weather, the stench of quackademic medicine at the NEJM was restored, at least in my memory, by an article that a reader sent to me. Apparently someone was interested in just who some of the writers of the NEJM article were. At the time, when I wrote about the article, I didn't really care too much about any of the authros other than the lead author, Dr. Brian Berman. Apparently this reader thought I should check out at least one of the other authors, which I proceeded to do. I happened to pick Dr. Helene M. Langevin of the University of Vermont. (Who knew Vermont had quackademic medicine?) One thing led to another (PubMed, specifically), and suddenly I found this gem of a quackademic medicine article by Dr. Langevin in, of all places PLoS ONE, entitled Electrical Impedance of Acupuncture Meridians: The Relevance of Subcutaneous Collagenous Bands. Senior author? Dr. Langevin. Funding source? What do you think? The National Center for Complementary and Alternative Medicine (NCCAM), of course! Read the rest of this post... | Read the comments on this post... Also check out the featured ScienceBlog of the week: Inside the Outbreaks on the ScienceBlogs Book Club

Archaeological chronology aims to answer the question "When did this or that event happen?". This question can usually be re-phrased as "When was this or that thing made?", where the thing under study may be anything from a bead up to the Great Wall of China. Most dating evidence is based upon similarity: people are almost incapable of doing anything in exactly the same way for any long stretch of time, and when they try to return to an old way of doing something, they never get all the details right. Such similarities (again on all scales of evidence) are dealt with in a more or less formalised way by means of a tool kit called typology. Collect a group of similar pots / house foundations / Great Walls, note explicitly the details that unite them and separate them from their peers, and you have a type definition. Thus defined, all types have a chronological delimitation, though many may be too long-lived to be very useful, and the presence of one type of pot doesn't rule out the parallel existence of several other types. The very birth of archaeology as a scientific discipline is reckoned from the first chronological and typological breakthrough: C.J. Thomsen's 1821 division of Scandinavian Prehistory into three Ages where cutting tools were made of different materials. First stone, then bronze, and then iron. Chronological research is still working to sub-divide the three Ages into ever finer well-defined slices. The definition of an archaeological period takes the form of a list of types found associated with each other: pots, houses etc. How can we know in what order these periods occurred? We still largely do this by typological seriation and stratigraphy. Seriation is a more or less formalised process where you order a collection of pots / houses / Great Walls according to similarity. You put two pots on a table, grab a third pot and decide if it should go between the two or over to either side. This is formalised as pot 1 having traits ABC, pot 2 BCD and pot 3 CDE. Then test if the series you've established is chronological, firstly by seriation of closed find associations (graves, hoards) by the same means, then by stratigraphy. Are ABC pot sherds usually in layers located on top of separate layers with CDE pot sherds? Or the other way around? Or are they usually mixed up? So far I've spoken only about relative chronology, where we can say with confidence that the types listed for period B fill the interval between periods A and C. What about absolute chronology, that allows us to say that the period B types appeared in the AD 10s and were replaced by period C types in the AD 150s? There are many methods, most importantly radiocarbon. Radiocarbon dating is a complicated field of research that moves forward rapidly. Briefly put it will tell you when a certain living thing died. With current technology, the accuracy is usually counted in decades. Much of the intricacies with radiocarbon have to do with the relationship between the death of that living thing and the event an archaeologist wants to date. If you find a piece of charcoal on a settlement site, you first need to think about how it ended up there. Stratigraphy is paramount: is it under a stone foundation? Or is it in a ditch that cuts across a house foundation? If you can't answer such questions, don't even submit the sample. And you need to think of intrinsic age: the heartwood of an old oak died centuries before someone cut the tree down. A wood anatomist can judge this for you. Bones have no intrinsic age, but their apparent age is skewed by the amount of seafood the creature ate in life. Other important absolute dating techniques are historical dating (e.g. coins with dates on them or the names of rulers whose regnal dates are known), dendrochronology (the width of tree rings varies with the weather, forming a chronological bar code) and thermoluminiscence (quartz in a brick or potsherd or hearth stone accumulates radiation energy after being set to zero by strong heat). Techniques like radiocarbon have not made typology or stratigraphy obsolete. For one thing, you need robust typological definitions to be able to generalise the radiocarbon date of a single object to an entire group of similar ones. Furthermore, fashion changes at shorter intervals than the current accuracy of a radiocarbon date. This means that you can often get a tighter date from typology than from radiocarbon. Southern Scandinavia's Migration Period lasted about 170 years and is thus about three radiocarbon dates long. But seriating a sample of female graves from Gotland, I managed to define four successive fashion phases for the same interval. For a more thorough treatment of the subject, see Kris's long post over at About.com. [More about archaeology, chronology; arkeologi, kronologi.] Read the comments on this post... Also check out the featured ScienceBlog of the week: Inside the Outbreaks on the ScienceBlogs Book Club

"The problem with American civil religion is that it reduces faith to a particular brand of nationalism, which is precisely the opposite of the message preached by Jesus and the prophets of the Hebrew Bible. By ignoring passages about social justice and community and highlighting appeals to individual liberties, Deuteronomistic theology, the Exodus, and conquest narratives, Beck attempted to weave together a generic, nationalistic religion that he hopes will appeal to the lowest common denominator of both faith and politics – personal ‘salvation’ via individual liberties – and overlook the more pervasive themes of social justice, equality, and community – which all people of faith are called to do! We are called to live together in community together as one body, not as rugged individuals."
-- Bob Cargill, in a post which rightly bears the title "excellent article on glenn beck’s call to a generic american civil religion"

I missed this earlier, but another of Glenn Beck’s Saturday stunts rips from the classic annals of demagoguery: Making a show of fear for one’s own safety dramatically conjures the specter of enemies, even if they don’t actually exist. This was, again, a stunt used to great effect by Augustus after he assumed sole mastery of Rome. When minting new Senators, to underscore the still-fresh memory of his adopted father’s death at the Body’s hands, and (by some interpretations) keep anger at the Senate alive, thus deferring the Republic’s restoration, the princeps conspicuously wore mail under his tunic, carried a sword, and was followed by bodyguards. See Suetonius, De Vita Caesarium, “Divi Augustus,” XXXV. That the demure father of his fatherland could still fear for his safety, after all the good he’d done, made the point better than any actual assassin could. Similarly, Beck’s decision to flaunt his bulletproof vest speaks to paranoia and persecution but omits any reasonable basis to believe it, or a credible threat, exists. The classier — but riskier move — is to trust. One searches history in vain for any record of Obama, or any American president, wearing a bulletproof vest.  Rumors that 44 wore a suit laced with bulletproof cloth are just that, and underscore rather than refute the point.

A topic of growing interest (and concern) at SBM is laboratory and diagnostic test pseudoscience. Bogus tests are everywhere, and Kimball Atwood recently discussed several of them. But over the past several years, diagnostic tests have emerged that appear to be science-based and offer gene-level insights into your health. And these tests don’t even require a physician’s visit – just a swab of saliva and a credit card get you reams of information on your genetics, traits, and risks of dozens of diseases. It looks like the ultimate in consumer health information, with the potential to offer truly personalized treatment strategies. Companies like 23andme, deCODEme, and Navigenics all promise “genetic insights” to improve your health. How could this information be anything but helpful? Personalized medicine describes medical practices that use information about a person’s genes, proteins, and environment to prevent, diagnose and treat disease. Science-based practice has routinely incorporated environmental advice (e.g., diet and exercise) into medical management. And there are a number of genetic tests in routine use that are well established, clinical validated, and are highly predictive of future outcomes, such as tests for Huntington’s disease and hereditary breast cancer. Predicting how well drugs will work is another area of personalized medicine. Cancer cells have specific genetic mutations that lead to uncontrolled growth. Identifying the mutation, and then developing drugs to target it, means more targeted treatments. Trastusumab (Herceptin) works only in patients overexpressing the Her-2/neu oncogene. Panitumumab (Vectibix) and cetuximab (Erbitux) effectively treat colorectal cancer, but only in patients whose tumors have wild-type KRAS oncogenes. And gefitinib (Iressa) a drug that initially didn’t look that promising, seems to offer a much better risk/benefit perspective in patients with EGFR mutations. Tumor testing for these specific genetic markers helps predict patient response, guides drug selection, and spares the costs and consequences of ineffective therapies. Whole-genome testing, offered directly to the public, is the latest development in personalized medicine. Companies typically offer to test for genetic traits that predict the risk of disease or estimate the effectiveness of drug therapies. In a typical test, up to a million single nucleotide polymophisms (SNPs) may be analyzed. A customized report is generated, describing the SNPs and your individual risk factors, usually based on population-level studies of what these SNPs mean. But our understanding of the correlation between SNPs and the risks they identify is still in its infancy. It’s fair to say we only have a preliminary understanding of the relationship between SNPs, environmental factors, and other influencers of illness. It’s not even clear that SNP variants provide meaningful information on risk, beyond what we already know. For example, a study published earlier this year concluded that adding ten additional genetic variants to to a standard breast cancer risk assessment model had little effect on improving the accuracy of predictions. It adds to a growing list of variants which don’t seem give us any actionable information. But the science doesn’t seem to be stopping the vendors of these tests from making unsubstantiated claims about their accuracy and relevance. The GAO and the FDA The US Government Accountability Office (GAO) recently released the results of an investigation into 15 companies offering DTC genetic testing. And it raised some serious questions about the accuracy and validity of information currently available to consumers. The GAO purchased ten tests from four companies, and sent duplicate samples to each company, changing the demographic information each time. The results were alarming: GAO’s fictitious consumers received test results that are misleading and of little or no practical use. For example, GAO’s donors often received disease risk predictions that varied across the four companies, indicating that identical DNA samples yield contradictory results. One donor was told that he was at below-average, average, and above-average risk for prostate cancer and hypertension. and Although the experts GAO spoke with believe that these tests show promise for the future, they agreed that consumers should not rely on any of the results at this time. As one expert said, “the fact that different companies, using the same samples, predict different directions of risk is telling and is important. It shows that we are nowhere near really being able to interpret [such tests].” GAO also found 10 egregious examples of deceptive marketing, including claims made by four companies that a consumer’s DNA could be used to create personalized supplement to cure diseases. Two of these companies further stated that their supplements could “repair damaged DNA” or cure disease, even though experts confirmed there is no scientific basis for such claims. One company representative even fraudulently used endorsements from high-profile athletes to convince GAO’s fictitious consumer to purchase such supplements. Two other companies asserted that they could predict in which sports children would excel based on DNA analysis, claims that an expert characterized as “complete garbage.” Further, two companies told GAO’s fictitious consumer that she could secretly test her fiance’s DNA to “surprise” him with test results–though this practice is restricted in 33 states. Perhaps most disturbing, one company told a donor that an above average risk prediction for breast cancer meant she was “in the high risk of pretty much getting” the disease, a statement that experts found to be “horrifying” because it implies the test is diagnostic. To be clear, this was not a scientific study, and the results can’t be interpreted to be a comprehensive analysis of the state of the marketplace. But they do give consumers and health professionals cause for concern. Not only did the investigation raise questions about whether these tests are are accurate, there is mixed information about what the results actually mean. The marketing goes well beyond the robust evidence that’s needed to draw stronger correlations between SNPs and specific risk factors. And while some companies are offering legitimate tests (albeit of questionable use), other companies are selling snake oil diagnostics, wrapped in a double helix. Not surprisingly, the FDA recently took action, sending warning letters to several companies, informing them that these tests require regulatory approval before they can be marketed. While the letters and the FDA’s intent has been subject to considerable scrutiny, the message is clear: the FDA intends to regulate this marketplace. Expert Opinion – Also Pessimistic If anyone should be enthusiastic about genetic testing, it would be Craig Venter, who was the first to sequence the human genome. Yet in an intriguing interview in Der Speigel magazine, he is decidedly skeptical about its utility, as noted in a few exchanges: SPIEGEL: Why is it taking so long for the results of genome research to be applied in medicine? Venter: Because we have, in truth, learned nothing from the genome other than probabilities. How does a 1 or 3 percent increased risk for something translate into the clinic? It is useless information. SPIEGEL: Do you think there will be a time when you can extract all this information to yield real medical results? Venter: For that to happen we need a lot more information: Information about your body’s chemistry, your physiology, your complete medical history, your brain and your entire life. We would need to do that a million times on different people and correlate that data with their genetic information. SPIEGEL: Will that lead in the end to the kind of personalized medicine that genetic researchers have always touted? Each person would get his or her own personal treatment that is tailored precisely to that person’s genetic make-up? Venter: That was another one of these silly naïve notions that was out there. It’s not, ‘Oh, we know your genome, we’re going to make this drug for you.’ That will never happen. It is more important that you use the information in the genome about your personal risks and reduce them through intelligent behavior. It’s anecdote, yes. But when one of the world’s leading scientists is this pessimistic, it doesn’t send a positive signal. The British Approach In the United Kingdom, the Human Genetics Commission is taking a different approach than the FDA. Rather than move forward with regulatory intervention, it recently published the Common Framework of Principles for direct-to-consumer genetic testing services, which supports industry self-regulation, while focusing on consumer interests. Here are the highlights: Scope: The framework is intended to ensure good practices; meeting consumer expectations while safeguarding their interests. The principles apply to tests ordered directly by consumers or by a non-medical intermediary. Marketing and Advertising: Validity claims should be supported by peer reviewed evidence, and references should be provided. This evidence must be presented fairly and transparently (i.e., no cherry-picking). Regulatory: Evidence for the association between a genetic marker and a disease, condition or trait identified in the test must be provided. “Associations should be validated at genome wide significance level in more than one large case control study and in a cohort of the ethnic/geographic background relevant to the client. The associations should be published in peer-reviewed scientific journals, they should be undertaken in line with the recommendations made in the STREGA statement, and the provider should supply standard references for these publications.” Accepted and transparent statistical methodologies should be documented to document how the risk of the disease, condition or trait was calculated. Information for Consumers: Clear and transparent information should be provided to consumers about the tests offered, their scientific basis, counselling offered, how samples will be handled post-test, possible consequences to future decisions (e.g., life insurance), etc. Data shall be presented in easy-to-understand formats. If a test provider intends to recommend products such as supplements, then information about lifestyle modification and other strategies should be provided. Depending on the type of test being offered, a health professional should oversee the information provided under this principle. Counselling and Support: “Where the test is a genetic test in the context of inherited or heritable disorders, that test should only be provided to consumers who are given a suitable opportunity to receive pre- and post-test counselling.” Consent: “A genetic test should be carried out only after the person concerned has given free and informed consent. Informed consent can only be provided when a consumer has received sufficient relevant information about the genetic test to enable them to understand the risks, benefits, limitations and implications (including the implications for purchasing insurance) of the genetic test.” “Genetic tests in respect of children when, according to applicable law, that child does not have capacity to consent should normally be deferred until the attainment of such capacity, unless other factors indicate that testing during childhood is clinically indicated.” Data Protection: All genetic information must be protected as per any other medical or personal health information. Sample Handling: All handling of genetic samples must be carried out in accordance with legal, medical and professional standards. Laboratory Processes: Laboratories performing tests should be accredited for quality assurance in molecular genetic testing. Interpretation of Test Results: Depending on the test, interpretation should be carried out under guidance of an appropriately trained and accredited professional. When information is provided related to risk assessment, the differences between relative and absolute risks should be made clear. Provision of Results: Information should be provided in an easy-to-understand format. When testing for conditions or traits, non-genetic factors should be identified. Continuing Support: Depending on the test, ongoing access to consultation should be offered. Complaints: A robust process for dealing with complaints should be in place. In order for the DTC market to avoid strict regulation, the Framework looks like a good place for the industry to start. It allows full access by consumers to their own genetic information, while requiring a full disclosure when any interpretation of that information is offered. Towards a Science-Based Approach Our access to genetic information currently exceeds our understanding of what that information actually means. The science underlying these tests is still evolving, and that means the interpretations of this data will continue to evolve. Until better and more conclusive data emerges to correlate SNPs with actual health outcomes, consumers will be dealing with probabilities that are largely irrelevant for health decisions. Luckily, there’s a more powerful and far simpler approach: You can make far more substantial reductions in your risk of cardiovascular disease, cancer, or diabetes without any genetic testing at all: simply follow science-based prevention and treatment guidelines.

As some of you have already noticed, I have turned comment moderation back off. The Internet terrorist who has been posring spam comments seems to want to force bloggers he disagrees with to moderate comments, presumably to hinder free discussion (with which comment moderation interferes). And giving in to what bullies want just encourages them to continue their behavior.

So comment moderation is off, and hopefully no one will find the occasional easily-recognizable spam message (which will always be deleted quickly from the blog anyy, so please don't respond to them) too much of a nuisance. It is a small price to pay for being able to discuss things and express ourselves freely.

Thanks!

The MMR vaccine, since it was wrongly and fraudulently associated with autism, has been a favourite of media scare stories concerning healthcare.  A recent example was the Main on Sunday’s recent story linking a legitimate and successful claim for compensation following a possible injury caused by the vaccine to autism, despite this forming no part of the claim nor the reasons given for its award. Both Evan Harris and Martin Robbins have good analyses of this story in the Guardian’s new science blogs section, citing statements by Nadine Dorries, MP, a member of the Health Select committee, suggesting that she, despite having responsibilities as a politician, in intent on fanning the dying embers of a seemingly settled controversy. Dorries has some ability to attract press attention thanks to questionable judgement and simplistic, and factually wrong, moral judgements but she shows little sign of being much of a threat to society’s understanding of healthcare via her political career.  She is not an obvious choice for any ministerial or lesser government role and has shown a reluctance to attend the meetings of any committee of which she is a member. However, the views of politicians can have an impact on healthcare.  Tony Blair, the former Labour Prime Minister, whose willingness to indulge his wife, Cherie’s, association with alternative health gurus, who are typically associated with anti-vaccination views, has been accused of giving credibility to opponents of MMR when he refused to say whether or not his son, Leo, born when he was in office, was vaccinated despite eventually issuing a statement following press attention. The reason we have refused to say whether Leo has had the MMR vaccine is because we never have commented on the medical health or treatment of our children. The advice to parents to have the MMR jab is one of scores of pieces of advice or campaigns the government supports in matters ranging from underage sex to teenage alcohol abuse or smoking, to different types of advice for very young children on a huge range of activities from breastfeeding to safe play.Once we comment on one, it is hard to see how we can justify not commenting on them at all. However, the suggestion that the government is advising parents to have the MMR jab whilst we are deliberately refraining from giving our child the treatment because we know it is dangerous, is offensive beyond belief. For the record, Cherie and I both entirely support the advice as we have consistently said throughout. It is not true that we believe the MMR vaccine to be dangerous or believe that it is better to have separate injections, as has been maliciously suggested in the press, or believe that it is linked to autism. We now know that, according to Cherie Blair’s autobiography, Leo was vaccinated and a Daily Mail report on Tony Blair’s autobiography suggests that the press were briefed off the record at the time that this was the case, although he appears to regret that he had not been clearer on this issue. Tony Blair is yesterday’s man though, and while his past actions may influence current events he is no longer a frame of reference for current UK politics.  He is out of parliament and out of favour with respect to his party, the press and the public.  We have a new government, a coalition between Conservatives and Liberal Democrats, whose views will now influence public health care.  Given that the Prime Minister, David Cameron, has a new baby it is inevitable that some questions of infant healthcare will be framed with reference to his new born daughter.  With this in mind it is worth considering his and his party’s previous views on MMR. In the past Cameron has stated that his children have had the MMR but that he supports the option of single vaccines if vaccine uptake continues to fall.  This support for single vaccines was a feature of the Conservatives when they were in opposition with the then shadow, and now current Health Secretary Andrew Lansley sharing these views.  Single vaccines are regarded as being no safer than the MMR vaccine, and carry additional risks with respect to intervals between vaccinations, and single mumps vaccines are now not licensed for use in the UK.  By contrast the Liberal Democrats, primarily via Evan Harris, then an MP, have supported the MMR vaccine as the best option. However, as supporters of the coalition government often argue, positions held in opposition are often lost in the compromises that come with the wielding of actual power and there is little sign that the current government is going to change policy on MMR, despite the Conservative Party’s previous views.  Jeremy Lefroy, a Conservative MP, recently asked the Health Secretary if he would ‘assess the merits of reintroducing a license for the single mumps vaccine?’.  The answer was to defer to the MHRA – which typically uses an evidence based approach to drug licensing and has opposed single vaccines in the past. The Daily Mail remain opposed to MMR, despite all the evidence of safety and the punishment inflicted on the disgraced Andrew Wakefield, and it would be wise of politicians not to give credibility to their views.  I hope that questions with respect to MMR will not be asked of Cameron, but that if they are he answers sensibly and in accordance with the evidence.

As predicted, Gaston has emerged from from the ITCZ as a named tropical storm in the eastern Atlantic. Unlike Fiona, Gaston will reach hurricane status, and in fact, there is a pretty good chance that Gaston will be a major hurricane. What matters, of course, is where it goes. In any event, formation of a hurricane and nearing land will not happen until Labor Day or later. Meanwhile, Earl, which during the night Thursday and early morning Friday will be turning with 100 knot winds off the coast of the Carolinas, is getting some special attention from NASA. Here's a picture NASA published just a few minutes ago:
AIRS infrared image of Hurricane Earl on Sept. 1, 2010, shows the temperature of Earl's cloud tops or the surface of Earth in cloud-free regions. The coldest cloud-top temperatures appear in purple, indicating towering cold clouds and heavy precipitation. Image credit: NASA/JPL-Caltech In case you wanted to see wind speed and vector data from within the hurricane, we have that for you as well: MISR image of Hurricane Earl captured on Aug. 30, 2010. The left panel of the image extends about 1,110 kilometers (690 miles) in the north-south direction and 380 kilometers (236 miles) in the east-west direction. Earl's wind speeds are shown in the right panel. The lengths of the arrows indicate the wind speeds, and their orientation shows wind direction. The altitude of a given wind vector is shown in color. Image credit: NASA/GSFC/LaRC/JPL, MISR Team Read the rest of this post... | Read the comments on this post...