Respectful Insolence

Remember my post about the genetics of autism last week? Remember how I predicted that the knives would come out from anti-vaccine loons? My original prediction was that Mark “Not a Doctor Not a Scientist” Blaxill would pull one of his usual brain dead attacks on genetic studies, such as his ” immaculate mutations” gambit.

I guessed wrong, apparently. It wasn’t Mark Blaxill who went on the attack first. Although Blaxill hadn’t tried his hand at a pseudoscientific deconstruction of this study as of Sunday afternoon, John Stone over at the anti-vaccine propaganda blog Age of Autism has already pulled this gambit. In a post epitomizing the arrogance of ignorance entitled Scherer of Nature Autism Gene Study Fails to Disclose Pharma Funding As Competing Interest, Stone lays this brain-meltingly stupid charge of a conflict of interest on the corresponding author of the Pinto et al study::

Prof Stephen Scherer who is the senior author of the autism gene study launched in Nature last week holds the ‘GlaxoSmithKline-CIHR Pathfinder Chair in Genetics and Genomics at the Hospital for Sick Children and University of Toronto. The title used to be ‘GlaxoSmithKline-CIHR Endowed Chair”, GSK being one of the defendant companies in the UK MMR litigation

What’s so hilarious about this little paragraph is that Stone is clearly completely ignorant of just what an endowed chair is and because of that he’s just completely humiliated himself by laying down a swath of burning stupid that has consumed everything in its path.

Basically, to create an endowed chair, a company or wealthy donor gives a university a lot of money, and the university sets up the endowed chair using that money. The interest and dividends from the fund used to set up the chair are put at the disposal of the holder of the chair to do research and scholarship as he or she sees fit. The reason such chairs are desirable is because an endowed chair gives a researcher a reliable supply of funding without the need to write grant proposals or a department chair a source of funds for various projects that doesn’t have to come out of the departmental budget. It often allows a researcher to do more exploratory work or a department chair to engage in various research and educational activities by doling out funds from the chair to his faculty, for example, to support pilot projects by young faculty. Once an endowed chair is set up, the donor usually has no say over who gets the chair or how the money for the chair is spent. Claiming that Professor Scherer’s holding the GSK chair at his institution is an insurmountable COI that needed to be reported is, quite simply, ridiculous to anyone in academia who knows what an endowed chair is. Clearly, Mr. Stone does not, although one commenter going by the ‘nym of Werdna does try to set Mr. Stone straight. It’s a rare thing indeed on AoA for a commenter to take a blogger to task like that, something that usually only happens when an AoA blogger makes a mistake too egregious even for some of the less nutty AoA readers.

Equally ridiculous is Mr. Stone’s lack of understanding of what a corresponding or first author is on a biomedical research paper:

While Prof Scherer’s departmental colleague Dalila Pinto is listed as lead author of the paper Scherer is listed as ‘correspondence author’ and he identifies himself as ‘senior author’ in Kevin Leitch’s LeftBrain/RightBrain blog.

Here’s a hint for Mr. Stone. The lead author of the paper is an honor usually reserved for the person who had the most to do with designing and doing the research. Most of the time the first author is the person who actually wrote the manuscript. On the other hand, the corresponding author of a scientific paper (at least a biomedical paper) is usually the author listed last or near last. More importantly for Mr. Stone’s criticism, the corresponding author and the senior author are nearly always one in the same, namely the author in whose laboratory and using whose funding the research described in the paper was performed. That’s it. That’s all those terms mean. There’s no inconsistency there. The terms are interchangeable. Mr. Stone would do well to learn a little bit about what he speaks before embarrassing himself so.

I’d be happy to educate him.

Comments

  1. #1 Matthew Cline
    June 14, 2010

    “immaculate mutations”

    Jesus Christ as a member of the X-Men?

    Claiming that Professor Scherer’s holding the GSK chair at his institution is an insurmountable COI that needed to be reported is, quite simply, ridiculous to anyone in academia who knows what an endowed chair is.

    Well, of course there’s a COI, since if there wasn’t a COI then Scherer would agree with the AoA crowd. Q.E.D.

  2. #2 A Hopelessly Naive Person
    June 14, 2010

    I’m sure that when Mr. Stone realizes his mistake he will issue a correction so as not to mislead his readers. Accuracy is very important to the people at Age Of Autism.

  3. #3 David N. Brown
    June 14, 2010

    I keep telling people on both sides of this: Even scientists who DO commit fraud don’t, as a rule, seem to have financial gain as a primary motive.

    I’ve also noticed, sometimes when AoA et al complain, it’s not even clear what was or was not disclosed, because the published text doesn’t include a COI statement either way.

  4. #4 Matt Roman
    June 14, 2010

    Another palm-to-face moment at AoA….

  5. #5 David N. Brown
    June 14, 2010

    @4,
    No, that would require introspection and a sense of personal honor. AoA’s regulars show neither. When presented with proof they are wrong, their standard responses are to ignore it, censor it, deny it and possibly to threaten to sue someone for not taking whatever they say at face value.

    I suspect, based on AoA’s handling of the autism-genetics issue, that they are being pushed toward the fringes even of the “anti-vax” movement. By comparison, Bryan Jepson, the last man standing at Thougtful House, has demonstrated the tactic of accepting genetic factors and trying to argue vaccine, GI, etc. under the “environmental factors” banner.

  6. #6 DLC
    June 14, 2010

    Uh, right… the brilliant researchers at AoA.
    They’re right up there with the brilliant scientists at the Discovery Institute.

  7. #7 Becky Fisseux
    June 14, 2010

    “Conflicting interests” is one of John Stone’s favourite bleats when anything doesn’t support his point of view.

    Amusingly, he consistently dismisses all of Wakefield’s conflicts of interest as irrelevant.

  8. #8 Rogue Medic
    June 14, 2010

    Does that mean that Jenny McCarthy has not one, but two, obvious conflicts of interest?

    She has the well regarded, even more so among among teenage males than overly trusting soccer moms, Endowed Chair Chest of Dow Chemicals.

    Her breasts are Dow endowed. Or did she go with a less punny brand?

    Does she have algae filled implants, in order to Green her money machine?

  9. #9 David N. Brown
    June 14, 2010

    Another contradiction of reality I just noticed:
    “GSK being one of the defendant companies in the UK MMR litigation”
    Litigation which was shut down, after the lawyers for the plaintiff said they couldn’t win, 6 years ago!
    He also describes Rutter as testifying for vaccine manufacturers, even though Jake at AoA admitted, when I confronted them with the libellous nature of their claims, that the only payments he received were from the LAB.

  10. #10 lurker
    June 14, 2010

    I doubt AoA care what academics think. They want to convince the public and then have the law changed, rather like cdesign proponentsists.

  11. #11 Anna
    June 14, 2010

    Ha, anti-vaxers and alties in general love to play six degrees of big pharma, and then no matter how tenuous the connection, announce GOTCHA! I once had a lengthy argument with someone who proclaimed a study tainted by Big Pharma because it was funded by CIHR, and a CIHR awards committee member had pharma funding. Not even a paper author – someone on the awards committee! Who almost certainly wasn’t even on the committee when the project got funding! Completely ignorant of how the funding process actually works, and totally refused to be educated. She’d connected Big Pharma to the study, no matter how tenuously, and that was good enough for her to dismiss it completely.

  12. #12 Gordon Pasha
    June 14, 2010

    Hello

    As a holder of an endowed chair, I can say that the situation is not as black and white as claimed. Universities want donors to continue donating and therefore there is subtle pressure not to upset donors, particularly by holders of chairs. To what extent can that subtle pressure can influence someone’s research is a highly individual-dependent matter…

    Regards
    Gordon

  13. #13 augustine
    June 14, 2010

    Did he take drug money or not?

  14. #14 JohnV
    June 14, 2010

    “and because of that he’s just completely humiliated himself ”

    The problem is that those of us who recognize how stupid he made himself sound already knew that. His echo chamber at AoA won’t recognize that, either because they’re simply uninformed, or because they choose to ignore the truth in order to pursue someone with deep pockets.

  15. #15 Brian Deer
    June 14, 2010

    I think you are a little unfair to Mr Stone. Anyone who has watched his “little professor” antics over the years recognizes that he’s a poorly-educated man, who, despite apparently having an autistic son, has shown no interest in autism, no interest in vaccines, no interest in the safety of children, no interest in medical research, indeed no interest in anything but burbling on with his nonsense about “conflicts of interest”. He wouldn’t know a conflict of interest if it bit him in the ass.

    The upside of this clown’s cavortings was a hilarious incident where he turned up to the conclusion of Wakefield’s GMC hearing, and when the chairman read out a paragraph, Mr Stone – literally – ran from the room, screaming “wrong study, wrong study”, as though five panel members, five QCs and all their teams had been sitting there for two years and failed to realize they were looking at the wrong document. It was so monstrously stupid that it came round again as hugely value-for-money.

    I speak with some experience, since Mr Stone is stalking me. A number of people have written to me to suggest that they believe his motivation is sexual: that he wants to be close to me, and can only achieve a sense of this online. I’m not sure, although he is plainly obsessed by me. It’s pretty creepy, I’ll admit, but I think Mr Stone is best understood as a living example of how autistic disorders, and allied conditions, such as pathological demand avoidance syndrome, psychopathy and whathaveyou, are genetic. Certainly, if you are aware of his behaviour, you can see how hard he would run from the idea that it was the expression of his own genetic makeup that lies behind his son’s disorder.

    From my own point of view, I don’t really care what he does. As a result of his activities, I get a lot of traffic to my website, and a lot of cooperation from people who have been involved in anti-vax antics, but now realize what a charade it all is. So, in that sense, he’s not only helping to make Age of Autism look ridiculous, he (like Wakefield) are now working for me.

    But I’m not sure it’s right to single him out in this way. Sure, he doesn’t know what an endowed chair is. He doesn’t know what any of it’s about. That’s not why he does it. He just has this compulsive disorder through which he tries to feel that he’s important by endlessly cobbling together bits of garbage that he’s Googled. I mean, for christsake, he found out that the guy had a GSK-endowed chair from the paper he’s claiming didn’t declare this. I mean, Jee-sus.

  16. #16 Rene Najera
    June 14, 2010

    I jokingly disclosed that I had a conflict of interest at a flu meeting when I mentioned that I benefited financially from the flu vaccine. See, I didn’t miss work, so I made more than the five bucks he vaccine cost me. Someonein the crowd took me serious enough to try to call me on it during the Q&A. So I don’t put much past some loons anymore… Their stupidity is ceasing to amaze me.

  17. #17 augustine
    June 14, 2010

    New study funded by the pharmaceutical and chemical industries show that poverty is genetic. Twins born to poor families both tend to become poor adults. Likewise, twins born to wealthier adults tend to become wealthier compared to their peers.

    While there is no known medical cure for poverty, scientists are furiously working on a treatment. Genetically engineered and modified foods can help alleviate the symptoms of poverty such a starvation and malnutrition.

    Media conglomerates are also working on a campaign in conjunction with WHO to get cable television and internet into every single home below the poverty line. This will allow those at most risk to stay up to date on their condition and seek medical help where appropriate.

    A vaccine may also soon be available for $10,000 for a series of 10,000 shots although it’s not certain who will pay for it.

  18. #18 jen
    June 14, 2010

    Brian Deer, you are hilarious. So Wakefield and Stone are “working for you?” I’m not sure what kind of looney DSM label would apply- maybe narcissist or histrionic? delusions of grandeur comes to mind…but you need to get a fucking grip. The genetics study is hilariously useless as even some of your own science people have pointed out on these posts. It is quite likely that these various mutations are present in the healthy population and mean absolutely nothing.

  19. #19 FreeSpeaker
    June 14, 2010

    “immaculate mutations” Is that a new anti-vax singing group?

  20. #20 Lawrence
    June 14, 2010

    Jen – because these individuals continue to put out such a wide-range of garbage related to the anti-vaxx world, they are in fact helping those of us who are trying to truly educate the populace. They make it easy for us to point out the logical inconstencies and fallacies that they peddle to the uninformed.

  21. #21 Jillian
    June 14, 2010

    But what I want to know is….

    does the holder of an endowed chair get an ACTUAL chair to sit in? Because otherwise, the name just seems to be grossly misleading.

  22. #22 Jeff Read
    June 14, 2010

    Jillian,

    A kitchen chair.

    But only after they break your throne and cut your hair.

  23. #23 Pablo
    June 14, 2010

    “But what I want to know is….

    does the holder of an endowed chair get an ACTUAL chair to sit in? Because otherwise, the name just seems to be grossly misleading.”

    I think that was actually the case in old England. When they talk about the “Isaac Newton Chair” at Cambridge, they are talking about his seat at the head table in the main hall (think of Hogwarts with the head table – Cambridge still has that type of arrangement). So whoever is is in the “Isaac Newton Chair of Physics” at Cambridge gets to sit in Isaac’s old seat. Or the current version of it.

  24. #24 Scott
    June 14, 2010

    Even scientists who DO commit fraud don’t, as a rule, seem to have financial gain as a primary motive.

    Ironically, one of the more prominent apparent exceptions to that rule is none other than Wakefield.

  25. #25 Mu
    June 14, 2010

    Jen, in case you missed it sitting on the loo for the past five years, Brian’s work seems to have been holding up to scrutiny much better than Wakefield’s and his friends at AoA. But we know, that’s only because of the conspiracy.

  26. #26 MikeMa
    June 14, 2010

    @Scott,
    The difference between Wakers and many other fraudsters and liars is that when exposed, some tend to be sorry and regretful about it while Wakers and his ilk dig in deeper and harder. Kind of puts me in mind of Monty Python’s knights. As each limb (fraud) is lopped off (uncovered) the knight threatens revenge even louder and more impotently.

  27. #27 T. Bruce McNeely
    June 14, 2010

    But what I want to know is….

    does the holder of an endowed chair get an ACTUAL chair to sit in?

    If I were named a Holder (as if), I would insist on one of these:
    http://gizmodo.com/5515094/the-ultimate-la+z+boy

  28. #28 Dr Aust
    June 14, 2010

    In the UK the holder of an endowed chair doesn’t typically get any endowment-derived research funds to spend; they just get their salary paid from the endowment income.

  29. #29 Brian Deer
    June 14, 2010

    Ha. “Jen” is another of these mindless haters, just drowning in their own bile. This is the kind of thing she sends me:

    “Dear Brian,

    “I sure hope you’re happy now.

    “Sincerely,
    Jen Leavesley”

    I guess she gets off on that somehow.

    Maybe if Jen wanted to get a grip, she would ask Nature just how many thousands of manuscripts are rejected for each one published.

    But, of course, Nature is run by Big Pharma stooges as well, I guess.

  30. #30 Matthew Cline
    June 14, 2010

    @augestine:

    New study funded by the pharmaceutical and chemical industries show that poverty is genetic. Twins born to poor families both tend to become poor adults.

    Ha. Ha. Ha.

    When talking about twins in the context of genetic studies, it’s implicit that they identical twins, not twins in general. If autism were entirely environmental then if twin had autism the other would have a 90% chance of having autism, regardless of if the twins were identical or fraternal. However, that 90% figure only applies to identical twins, not fraternal twins.

  31. #31 RitzBitz
    June 14, 2010

    “But what I want to know is….

    does the holder of an endowed chair get an ACTUAL chair to sit in? Because otherwise, the name just seems to be grossly misleading.”

    I work for a med school and I just recently found out that an actual chair is awarded. The boss of one of my friends here just received one a couple months ago.

  32. #32 Marc
    June 14, 2010

    Don’t be so hard on Jen. After all, it’s clear that the conspiracy is that all of the medical-industrial complex circles the wagons to protect its gravy train. Except when it comes to brave insiders like Wakers and Jay Gorden, then it doesn’t. Then it circles the wagons against its own because they speak TEH TRUTH!1!!!

    But I must admit that the bigger laugh was Jen saying that the study was considered useless because…it means that we don’t have all the answers? This is truly like watching the virus version of Discovery Institute.

  33. #33 David N. Brown
    June 14, 2010

    @24, 26,
    Even with Wakefield, I am skeptical of the explanatory value of “profit motive”. I am inclined to think that he is more strongly influenced by a narcissist-type need for attention. To me, his tenacity in defending his hoax is a point against prosaic greed. It would have been in his overall best interests to agree with his peers in retracting his study (with a “spin” about needing more research). That, I think, would have prevented the in-depth scrutiny that exposed his work as completely fraudulent.

  34. #34 MikeMa
    June 14, 2010

    David @33
    You may be correct about Wakefield now but his trial lawyer money and the competing vaccine early on definitely point to a profit motive. Power and prestige certainly, but money too.

  35. #35 Matthew Cline
    June 14, 2010

    I am inclined to think that he is more strongly influenced by a narcissist-type need for attention.

    Or maybe (for whatever reason) he thinks that multivalent vaccines and/or the current attenuated strain of measles must cause some sort of problem, and that’s why he’s sticking to his guns. He’s blamed MMR for Crohn’s disease and ulcerative colitis before he blamed it for autism, it’s just that now that he’s blamed autism he has a lot more supporters.

  36. #36 Enkidu
    June 14, 2010

    LOL at the corresponding Vs senior author “discrepancy.” I think that someone should throw in the word “PI” (principal investigator) too to really confuse him!

  37. #37 Zetetic
    June 14, 2010

    So I see augie’s guilty of committing yet another Genetic Fallacy. Not to mention deliberately trying to ignore evidence and instead (oh so ironically) conflate actual evidence with the argument that correlation doesn’t equal causation (something anti-vaxers have trouble applying to vaccines).

    Is wittle augie building another wittle Straw-Man?

    Still waiting on evidence there augie…

  38. #38 Zetetic
    June 14, 2010

    @ everyone else:
    Wait until augie finally gets to claiming that his/her anti-vax beliefs are “religious” in nature, and how it’s the big bad atheists that are trying to save people’s lives through vaccination.

    It’s truly hysterically funny!
    ;-)

  39. #39 Enkidu
    June 14, 2010

    From Mr. Stone’s article: “The 176 authors undoubtedly escaped having to make more detailed disclosures of competing interest by publishing in Nature rather than one of the journals now signatory to the International Committee of Medical Journal Editors ‘Uniform Requirements for Manuscripts’.”

    Yes, because it is sooooooo easy to get a paper accepted in Nature. I mean, it’s not a TOP 3 journal or anything. Scientists just publish there because of their lax disclosure policy!

  40. #40 Nescio
    June 14, 2010

    Jen wrote:

    It is quite likely that these various mutations are present in the healthy population and mean absolutely nothing.

    Actually, one of the things that impressed me most about this study is that “a total of 226 validated de novo (7) and inherited (219) CNVs not observed in controls and affecting single genes were found.” That is 226 of these mutations appeared only in the ASD group and not at all in the 1,981 controls i.e. in the healthy population. Maybe “quite likely” means something different to you than it does to me.

  41. #41 Matthew Cline
    June 14, 2010

    Wait until augie finally gets to claiming that his/her anti-vax beliefs are “religious” in nature, and how it’s the big bad atheists that are trying to save people’s lives through vaccination.

    He’s done that before? I don’t remember that. What post did it happen on?

  42. #42 David N. Brown
    June 14, 2010

    @39,
    “`The 176 authors undoubtedly escaped having to make more detailed disclosures of competing interest by publishing in Nature…’”
    What Stone is effectively doing is conceding that Scherer may have disclosed as much as the journal asked for. (See comment 3)

    This paper looks like an egregious abuse rising from the tendency of professionals to “pad” their bibliographies. IgNobel prizes have gone to two even more extreme examples: a 1993 paper with 972 listed authors, and Yuri Struchkov, who got himself listed as author of 948 papers, possibly by abusing his control over specialized machinery. I think the two “Thorsen” studies AoA has been fussing about could similarly represent cases of someone getting credit more through bureaucratic maneuvering than legitimate contribution. But, once again, anti-vaxxers would rather build conspiracy theories than comment on real but prosaic problems.

  43. #43 Gr8GooglyMoogly
    June 14, 2010

    I love it when Jen goes all ‘get a fucking grip’ on us… as if she has one herself. Hi Jen… grip this…

  44. #44 Dangerous Bacon
    June 14, 2010

    Speaking of Jay Gordon, Maverick M.D. (as someone did earlier), he hasn’t yet commented on his website about the genetics paper.

    However, he has a fabulously trenchant commentary up about the recent Autism One conference, as follows (in its entirety):

    “I spent Saturday at an incredible conference in Chicago. Any thoughts I ever had about wavering in my support of Andrew Wakefield have dissolved.”

    Brilliant! By “wavering”, does Jay mean he regrets having previously expressed a slightly dim view of the quality of Wakefield’s Lancet publication, and has now become a total Wakefield groupie like the rest of the AoA crowd?

    Dr. Jay should have his own endowed chair in the field of antivax lunacy – an Off Your Rocker.

  45. #45 Marilyn Mann
    June 14, 2010

    I don’t find fault with him for not knowing what a corresponding author is, but I do find fault with him for blathering on about shit he knows nothing about.

  46. #46 bensmyson
    June 14, 2010

    So does this mean that all those with autism have this CVN mutation thing or only a few of them (200 out of 1,000)? And zero of the non-autistic group? Zero?

    Do vaccines cause gene mutations? Anyone know if there is a study on that?

  47. #47 Werdna
    June 14, 2010

    Orac mentioned me in his blog. Cool! Just to clarify I’m not actually your typical AoA commenter. I consider virtually everyone there to be a crank. There are only a few comments by me on AoA and in case anyone actually looks. There is one which contains some of the greatest stupid known to man. This was a bit of an experiment wrt AoA moderation. I made two posts under two different names to the same thread. One had a series of unambiguously true statements which were counter AoA dogma and another which had some false statements which would be exceptionally difficult to perceive as true but were in-line with my perceptions of AoA dogma – both were posted to the same article. Only the one which agreed with AoA dogma actually was allowed. I’ve often wondered if one could perform with with a much larger sample if it wouldn’t result in some kind of “crank index”. Essentially the probability to reject something which is categorically true but supports some assertion you reject or to accept something which is categorically false but is supports some assertion you agree with.

    @Gordon

    I’m sure you know better than I but as someone who also works at an educational institution I’d highlight two things. Often an industry endowed position involves an investment which lasts multiple years. I think this particular Chair comes from a $1M investment by GSK. So although I’d agree that my university would like someone like GSK to continue to donate money. This seems to differ significantly from getting your paycheck from GSK.

  48. #48 sarkeizen
    June 14, 2010

    “New study funded by the pharmaceutical and chemical industries show that poverty is genetic. Twins born to poor families both tend to become poor adults. Likewise, twins born to wealthier adults tend to become wealthier compared to their peers.”

    I’ll assume Augustine is making a comment on the twin studies used as evidence to the heritability of autism. If so, you would notice that many of these studies compare MZ – mono-zygotic (Identical Twins) and DZ – Di-zygotic (fraternal twins). The results are significant because MZ twins have a HIGH concordance when the DZ twins DO NOT – meaning that the higher degree of genetic correspondence is met with a higher degree of incidence.

    However in your example. MZ and DZ twins born to poor households are just as likely to “inherit” poverty.

    So not only was your post unfunny (except possibly to be laughed AT) it was also untrue. BraVO!

    Aside: Kind of interesting that Jenn the implicitly (but not explicitly) self-determined genetics expert is now just boring and vitriolic.

  49. #49 Chris
    June 14, 2010

    a parent of Ben:

    Do vaccines cause gene mutations? Anyone know if there is a study on that?

    How would that work? Who getting the vaccine causes the mutation? The father, the mother or the child?

    Out of the following environmental factors that I experienced as a youth in the 1960s, which ones are a less likely trigger for gene mutation than vaccines:

    lead from leaded gasoline and lead paint
    cigarette smoke (the house was a blue haze)
    getting covered in Mercurochrome for chigger bites
    getting chicken pox
    getting mumps
    getting influenza, pneumonia, and other various illnesses
    being exposed to bug spray
    playing with mercury from a broken thermometer
    diesel fumes from the boat
    ….

    These were typical things that any kid up through the 1970s and even into the 1980s would have been exposed to. I’d really like to know how they could have caused less impact to human biochemistry than any vaccine.

  50. #50 Calli Arcale
    June 14, 2010

    Ben’s Parents:

    So does this mean that all those with autism have this CVN mutation thing or only a few of them (200 out of 1,000)? And zero of the non-autistic group? Zero?

    In the study, it was a strong correspondance between having autism and having copy number variations in these critical areas — meaning most of the studied autistic children did indeed have them. However, the study did not look at every child on earth; it is too early to extrapolate to the general population what percentage of autistic patients were genetically predestined to become autistic.

    Do vaccines cause gene mutations? Anyone know if there is a study on that?

    Like all new drugs, vaccines and vaccine ingredients are studied for safety. There is no evidence they are mutagenic in the doses used.

    The particular variations observed in autistic patients vary. Not all are heritable; I seem to recall reading that 5% of the ones found in this study were de novo, meaning it was a spontaneous mutation in one parent’s germline cells (the cells that become sperm and eggs). Germline mutations are actually not that uncommon; in fact, they’re crucial for evolution of a species. They also tend to increase with parental age.

    The genes they found in this study could not have been caused by vaccines; they are clearly heritable, and in most cases, *were* inherited. (They did not just sequence autistic people; they also sequenced their first-order relatives.) It’s not faulty expression of genes; it’s having the “wrong” genes to begin with. (Scare quotes are there because I’m not sure it’s possible to say which genes are the *right* ones in the first place. People are supposed to be different, after all.)

    This does not rule out some epigenetic effect, or the much-vaunted “genetic susceptibility to vaccines” that AoA et al are often pushing. What it shows is that there is a very strong correspondence between certain genetic differences and autism. Also, it appears to involve quite a large number of genes, so the condition is complex, and likely to manifest differently in different patients. Which is in fact what we see. This does not rule out vaccines having some role; that question was not explored in this study. But it does show that there is a very clear genetic role.

  51. #51 Janet Holmes
    June 14, 2010

    Well thanks for explaining that cause I didn’t know wtf she was on about!

  52. #52 augustine
    June 15, 2010

    Chris: “These were typical things that any kid up through the 1970s and even into the 1980s would have been exposed to. I’d really like to know how they could have caused less impact to human biochemistry than any vaccine.”

    Somehow, I believe this is a logical fallacy. Just somehow. Where o where are the critical critical thinkers to show Chris the error in his ways?

    O champion of logic where art thou?

  53. #53 augustine
    June 15, 2010

    Callie: “There is no evidence they are mutagenic in the doses used.”

    Is that specifically studied, Callie?

    Are you being disingenuous?

  54. #54 David N. Brown
    June 15, 2010

    @47:
    “I made two posts under two different names to the same thread. One had a series of unambiguously true statements which were counter AoA dogma and another which had some false statements which would be exceptionally difficult to perceive as true but were in-line with my perceptions of AoA dogma – both were posted to the same article. Only the one which agreed with AoA dogma actually was allowed.”
    I’d be very interested to see these.

    I have wondered if AoA censors comments not JUST to prevent errors and flat-out lies from being corrected in a timely way, but to hide how much of the traffic they get is from their own critics. I think it’s very possible that, if they were forced to allow every comment to appear (and I think they should be), commenters correcting their claims and generally denouncing their movement would outnumber “friendly” readers by at least 2 to 1. Then their sponsors might respond by cutting payments proportionately.

  55. #55 Zetetic
    June 15, 2010

    Matthew Cline @ #41:

    He’s done that before? I don’t remember that. What post did it happen on?

    I’m not surprised that you (and probably many others) missed it. It was at the end of a long back-and-forth between augie and myself (with some input from a few others). Augie tried to set up a very predictable false dichotomy between “religious” anti-vaxers and the (according to augie) atheist pro-vaxers. Ignoring of course the religious that support (or develop) vaccines as well as the occasional atheist anti-vaxer.

    The link is here…
    Age of Autism and vaccination against meningococcus: augustine post #280
    My own response is the second post down from there.

  56. #56 Zetetic
    June 15, 2010

    one of Ben’s parents:

    Do vaccines cause gene mutations? Anyone know if there is a study on that?

    Aside from what the others have already said there is the question about why do those that haven’t been vaccinated get autism?

    If it’s the parents that were mutated by the vaccines, then what about the de novo mutations in the children that weren’t inherited from the parents?

  57. #57 Matthew Cline
    June 15, 2010

    Do vaccines cause gene mutations? Anyone know if there is a study on that?

    IIRC, medication is only tested for mutagenic effects if one or more of its ingredients is mutagenic. I’m guessing that there’s few (if any) vaccines which have any muatgenic ingredients, so there’s probably not any studies in that area. As for whether or not a combination of chemicals can be mutagenic when non-mutagenic in isolation, well, I’m not a biologist or biochemist, but I don’t think that happens.

    Anyone with more knowledge in this field, please correct me if I’m wrong.

  58. #58 Werdna
    June 15, 2010

    @52

    “I have wondered if AoA censors comments not JUST to prevent errors and flat-out lies from being corrected in a timely way, but to hide how much of the traffic they get is from their own critics. I think it’s very possible that, if they were forced to allow every comment to appear (and I think they should be), commenters correcting their claims and generally denouncing their movement would outnumber “friendly” readers by at least 2 to 1. Then their sponsors might respond by cutting payments proportionately.”

    I agree that having posted there for a few weeks under different names they are at best mildly tolerant of certain opposing views. I’d question if this is some direct monetary correlation though. Knowing something about they way compensation is paid out for online advertisements even if there are twice as many pro-science folk as anti-vaccine folk reading/commenting (and most of the pro-science folk get deleted). They would probably get the same number of views and click-throughs.

    I could come up with a hundred theories for the draconian moderation there:

    - Maybe they think opposing views would reduce the number of believers – for which there is some evidence to the contrary
    - Perhaps they view this kind of censorship as tit-for-tat to the way Wakefield was censored (It’s interesting to see just how little criticism of Wakefield is allowed on that board. Even things like “He’s just not that smart” are not allowed).
    - Perhaps they are just angry..
    - All of the above? Who knows?

  59. #59 bensmyson
    June 15, 2010

    So this study proves what? That there is a likelihood that somehow there is an underlying genetic cause to autism? But not everyone with this genetic combination of mutations and abnormalities has autism right?

    Astonishing breakthrough?

    Oh well, Im sure it’s the beginning of something that will lead us somewhere else in about 5-10 years.

  60. #60 Visitor
    June 15, 2010

    “Perhaps they view this kind of censorship as tit-for-tat to the way Wakefield was censored (It’s interesting to see just how little criticism of Wakefield is allowed on that board. Even things like “He’s just not that smart” are not allowed).”

    How was Wakefield censored? By whom? When?

  61. #61 Marcus Hill
    June 15, 2010

    @23:
    There isn’t an Isaac Newton chair, but the chair which Newton held, the Lucasian Chair, is now held by Stephen Hawking. It’s not the same physical chair since, to quote Hawking, “in Newton’s day it wasn’t motorised”.

  62. #62 SteveF
    June 15, 2010

    Actually, the current Lucasian Chair is Michael Green.

  63. #63 SkydiverIM
    June 15, 2010

    “I am inclined to think that he is more strongly influenced by a narcissist-type need for attention.”

    “Or maybe (for whatever reason) he thinks that multivalent vaccines and/or the current attenuated strain of measles must cause some sort of problem, and that’s why he’s sticking to his guns.”

    Watching Waker`s Matt Lauer interview, he struck me as an arrogant fella, and I wonder how much his continuing motivation has changed from whatever it was in the beginning, to a fear of losing face. He has been digging his heels in deeper and deeper, in spite of having had many opportunities to back out or modify his position. I suppose it is possible he believed he was doing the right thing in the beginning, despite the glaring COI`s, but I suppose it is just as likely that he didn`t think anyone was clever enough to catch him. That would be admitting that there are people out there smarter than he is.

    It is also entirely reasonable that I am wrong about the motivations of a man I have never met.

  64. #64 Calli Arcale
    June 15, 2010

    Matthew Cline:

    IIRC, medication is only tested for mutagenic effects if one or more of its ingredients is mutagenic.

    I believe you are correct. The ingredients have all been tested, and there is no evidence of them being mutagenic, and so no reason to presume the vaccines to be mutagenic. And even if they were, it couldn’t explain the copy number variations seen in this study unless the mutations occurred in the parent’s germline cells.

    A mutation doesn’t automatically affect the entire body or get passed down to the next generation. Initially, it affects only the cell that got mutated. The cell may eventually divide, passing on the mutation, assuming the mutation isn’t a fatal one. But neighboring cells aren’t mutated, and cells clear across on the other side of the body aren’t mutated either, or if they are (having also been exposed to a mutagen), they aren’t mutated in the same way. Unless one of these cells happens to be in the germline, the mutation will not be passed on. If one of these cells are in the brain, you’ll probably just end up with one or two faulty brain cells and the rest will be perfectly fine; a loss of one or two cells is really insignificant on the scale of the brain, and it can route around them.

    In order for a non-inherited mutation to affect the entire brain or a significant portion of it, the mutation would have to have occurred before the embryo had finished differentiating. In other words, in the first few days after conception. Possibly up to a week or so, though the later we get, the less influence a mutated cell can have — with one exception. Mutated cells, if they lose their normal growth inhibitions, can become cancer. But that is definitely not the same thing.

    So even if vaccines were mutagenic, a vaccine given to a child cannot possibly account for the specific CNVs found in these children, because mutations do not affect every tissue in the body equally. It’s not like Marvel Comics, alas.

  65. #65 Militant Agnostic
    June 15, 2010

    Calli Arcale @63

    So even if vaccines were mutagenic, a vaccine given to a child cannot possibly account for the specific CNVs found in these children, because mutations do not affect every tissue in the body equally. It’s not like Marvel Comics, alas.

    So that’s where the anti-vaxxers get their scientific knowledge, especially regarding genetics.

    Calli – you are brilliantly insightful as usual.

  66. #66 Werdna
    June 15, 2010

    “How was Wakefield censored? By whom? When?”

    This is just conjecture on my part. I assumed that the withdrawal of his articles (in Lancet and Neurotoxicology) are interpreted as some form of censorship. But who knows what the crazies think.

  67. #67 Composer99
    June 15, 2010

    The augie troll shows off his logic chops and they end up looking pretty spindly (yet again):

    augustine @ 52:

    Chris: “These were typical things that any kid up through the 1970s and even into the 1980s would have been exposed to. I’d really like to know how they could have caused less impact to human biochemistry than any vaccine.”

    Somehow, I believe this is a logical fallacy. Just somehow. Where o where are the critical critical thinkers to show Chris the error in his ways?

    O champion of logic where art thou?

    Somehow, I am certain you are wrong.

  68. #68 Orange Lantern
    June 15, 2010

    It’s not like Marvel Comics, alas.

    Sure it is. Remember the VAERS report of the man Hulking out?

    http://neurodiversity.com/weblog/article/14/

  69. #69 Chris
    June 15, 2010

    It is a variation of the question that Little Augie has been asked several times and has refused to answer: the evidence that vaccines are more dangerous than the actual diseases.

    I am amazed at what all the parents who were born in the 1970s and later are freaked about. I remember when lead was removed from gasoline, getting the actual diseases, and living in a house with a blue haze because my mother was addicted to tobacco (yes, I remember my brother and I trying to get her to quit by hiding her cigarettes and the resulting manic that set it!). Not to mention the wanton and irresponsible use of pesticides on the food we ate (I went to an edible garden talk on pesticides, some of methods used in the 1960s are horrifying).

    And yet these younger parents (and little Augie) are freaked by teeny tiny bits of viral particles in vaccines.

  70. #70 Journal Checker
    June 15, 2010

    You are all being very unfair to John Stone. He is an expert published musicologist. Do please check his credentials. One might want to say that he should spend more time discussing Mozart and Beethoven and less on MMR, but that’s his choice.

  71. #71 trrll
    June 15, 2010

    One common assertion by those who buy into the vaccine causality obsession is, “You can’t have a genetic epidemic!”

    Now of course, we don’t in fact know that there is an epidemic of autism. A lot of the apparent increase is clearly diagnostic substitution, but that may not be the whole story. Even among genuine autism researchers and therapists, many consider it possible that there could be a genuine increase in incidence.

    But is it true that there can’t be a genetic epidemic? Since the 1950′s, we’ve had increasing penetration of women into the workplace, including scientific and technical fields. Many people on the Asperger’s end of the autistic spectrum have affinity for science and technology. I’d estimate that perhaps 30-50% of my classmates at MIT had at least some Asperger’s traits. What if the gene mutations or duplications that result in high ability in scientific/technical/mathematical fields also increase risk of autism in offspring? It is certainly plausible that a moderate gene dosage for a particular gene could be beneficial, while a greater dosage could be detrimental. There is certainly some evidence that autism in children tends to be associated with high parental IQ (although as with the increased incidence, it is hard to be certain that this is not a selection artifact). With the rise of high-tech industries, and with more women working in such industries, there is more opportunity for men and women with genetic traits that favor success in these industries to meet and marry. Could there be a genuine increase in autism resulting from changes in mate assortment?

  72. #72 RJ
    June 15, 2010

    @70

    Do not forget that GenX (in the U.S. and Europe) is waiting longer to get married and have kids (often for education/career). Other genetic anomalies, such as Downs syndrome, where there is an extra chromosome (as opposed to CNVs which are chunks of chromosomes), increase in occurrence with age of the parents. It is very possible that an increase in the number of CNVs, due to an increase in parental age, may have some role in the possible increase in the numbers of children diagnosed as on the spectrum.

  73. #73 Austin Elliott
    June 15, 2010

    John Stone and his mate Clifford Miller are having a tag-team pop at Orac over at the website of British newspaper the Guardian. See the comments here.

  74. #74 Composer99
    June 15, 2010

    Shoot. Blockquote fail in my comment 66.

  75. #76 augustine
    June 15, 2010

    Chris: “It is a variation of the question that Little Augie has been asked several times and has refused to answer: the evidence that vaccines are more dangerous than the actual diseases.”

    I haven’t answered it because it is a straw man argument.

    Your “people just need to toughen up” act is akin to the person who smokes a pack a day and doesn’t have cancer and says “Smoking doesn’t cause cancer”. “Only sissies get cancer.”

    Chris: “I love the smell of napalm in the morning.”

  76. #77 Zetetic
    June 15, 2010

    augustine @ #52:

    Somehow, I believe this is a logical fallacy. Just somehow. Where o where are the critical critical thinkers to show Chris the error in his ways?

    So listing other possible causes for a hypothetical “environmental trigger” is considered a fallacy by you augie? How amusing, exactly what fallacy is listing other purely hypothetical causes? As usual, augie, you don’t seem to know what a logical fallacy actually is, or what makes it a fallacy.

    O champion of logic where art thou?

    There are plenty here “O Sir Robin of Logic”. You’ll notice that the pro-vaxers will often criticize each other for making mistakes, when there is one being made. It’s the anti-vaxers that rarely criticize their own. (Because it’s the “cause” that matters, right, augie?)

    ===========================================================================================================

    augustine @ #53:

    Is that specifically studied, Callie?

    Why bother citing any such for you augie? It’s not like you’ll actually read it, you’ve already made that clear by not actually reading the links we’ve provided in the past. Try looking it up for yourself. Better yet, why don’t you show us evidence that they are mutagenic at the doses used in a vaccine?

    Are you being disingenuous?

    No augie, we all know that’s your job here. No one but your fellow anti-vaxers want to impinge upon your turf.

  77. #78 trrll
    June 16, 2010

    @augustine:

    I haven’t answered it because it is a straw man argument

    Clearly, you don’t understand what a straw man argument is. Here.

    Pretty much everything we do in life carries risks as well as benefits. About 5,000 people per year die from food-borne illnesses. Yet we continue to eat, because the benefits of eating outweigh the risks. You don’t even have to quit eating to avoid food borne illnesses, because you can eliminate the risk by the simple expedient of boiling everything you eat for an hour or so. Yet we don’t do that either, because most people feel that the benefits of things like raw vegetables outweigh the risk. Every time you get in an airplane or a car, you weigh the benefit–often merely convenience–against the risk of death in a fiery crash.

    So when somebody points to the risks of a course of action, it is only reasonable to ask whether they have properly weighted those risks against the benefits of that action and the risks of alternative courses of action. Evading the issue (as you do when you declare it to be a “straw man”) is evidence of either irrationality or dishonesty.

  78. #79 Zetetic
    June 16, 2010

    augustine @ #76:

    I haven’t answered it because it is a straw man argument.

    Really? So you haven’t been the one posting under “augustine” arguing that “healthy” people don’t need the MMR vaccine because the odds of surviving measles are so much better for them? I noticed BTW that you still never provided evidence (or a clear definition of “healthy”) to support that assertion.

    Your “people just need to toughen up” act is akin to the person who smokes a pack a day and doesn’t have cancer and says “Smoking doesn’t cause cancer”. “Only sissies get cancer.

    Coming from someone that claimed that the MMR shouldn’t be used since since only the unhealthy have anything to fear from measles, or that we shouldn’t be waging “war” with microbes, that is amusingly hypocritical of you augie. Not surprisingly hypocritical mind you (in fact it’s typical of you), just amusingly hypocritical.

    It’s especially hypocritical of you since that clearly wasn’t Chris’ point, and you are in fact the one creating yet another Straw-Man. Chris’ point was simply that it’s irrational to worry about vaccines being the culprit behind autism when there are far more likely hypothetical environmental triggers, ones that haven’t been tested for an association with autism. The anti-vaxers prefer to ignore those other possible triggers in order to focus on blaming vaccines regardless of how many studies show no association with autism.

    But then again, augie, I suspect that you already knew that, you just seem to never pass up the opportunity to make another Straw-Man argument.

  79. #80 augustine
    June 16, 2010

    trill: “Clearly, you don’t understand what a straw man argument is. Here.”

    I know exactly what a straw man argument is. And this is a straw man argument pure and simple.

    Is it possible that many on here are so blinded by their own ideology of force(some may prefer coercion) mass vaccination that they can’t see any other views or arguments therefore they conclude that this version of risk vs. benefit is the only equation possible? Yes. I find it amusingly hypocritcal that these same ones view themselves as scientific and consequentially objective and free from bias.

  80. #81 Chris
    June 16, 2010

    Little Augie, why is it so important that vaccines be blamed for autism? Why are vaccines a more likely culprit than breathing fumes from a car running on leaded gasoline or the haze of a cigarette smoke filled home or eating produce covered in now banned organophosphate pesticides as was common for many children growing up in the 1960s?

    (an aside, I am reading The Poisoner’s Handbook by another Scienceblogger Deborah Blum, it is amazing what very seriously dangerous poisons were available in grocery stores not too long ago!)

  81. #82 Journal Checker
    June 16, 2010

    I see the ticket only book signing session with Dr Andrew Wakefield will be hosted by an independent TV programme production company – Objective Productions.

    Here’s the listing:

    An Audience with Dr Andrew Wakefield

    Thursday 17th June 6.00pm – 9.30pm

    Objective Productions

    3rd Floor, Riverside Building, County Hall, Westminster
    Bridge Road,

    London SE1 7PB

    The event is scheduled to begin with a book signing of
    ‘Callous Disregard’ from 6.00pm. The main event ‘An Audience with Dr
    Andrew Wakefield’ will be from 7.00pm – 9.30pm.

    Tickets cost £25 per person and can be paid by credit
    card or by cheque.

    Please call 0208 979 2525 to confirm your place and
    method of payment.

    Entrance will be strictly limited to those who have pre-booked.

  82. #83 augustine
    June 16, 2010

    “Little Augie, why is it so important that vaccines be blamed for autism?”

    Old feller Chris who “knows everything because he’s been around the world in the military and held mercury in his hand and didn’t die”, it’s not that important. What I noted was your fallacious reasoning and lack of logic. No matter how dangerous mercury, unleaded gasoline, or napalm is it doesn’t make vaccines any safer or dangerous because of your relative comparisons.

    I’m sure you’re a smart guy. You should know this.

  83. #84 Chris
    June 17, 2010

    Little Augie:

    I’m sure you’re a smart guy.

    I know you are not smart. Because in that statement you used two words to describe me. Since you seem to stalk me on this blog you would know one of these words does not really describe me. What is worse, is that others have pointed it out to you. :

    1) smart

    2) guy

    Now figure it out. Not that I really care, I just think it is really funny.

  84. #85 Zetetic
    June 17, 2010

    augustine @ #83:

    What I noted was your fallacious reasoning and lack of logic.

    Actually augie you’re the one that used fallacious reasoning to distort what Chris has actually said in this thread, not that I expect you to ever admit the mistake.

    Since you seem to think that Chris is being unfair in suggesting that if there is an environmental trigger to autism, do you have any evidence (yes, I know that you don’t care for the “E” word) that supports a connection between vaccines and autism?

    BTW augie, have you been able to name the specific fallacy that applies to listing a possible cause for a hypothetical “trigger” for autism?

  85. #86 ArtK
    June 17, 2010

    @59

    So this study proves what? That there is a likelihood that somehow there is an underlying genetic cause to autism? But not everyone with this genetic combination of mutations and abnormalities has autism right?

    Astonishing breakthrough?

    Oh well, Im sure it’s the beginning of something that will lead us somewhere else in about 5-10 years.

    You’ve summarized it pretty well, except the “breakthrough” part. It’s just another piece of evidence in understanding the causes of autism.

    That’s the way science works. Little bit by little bit. The “astonishing breakthroughs” happen very, very rarely. That’s especially true when you’re working on something that appears to be extremely complex.

    I got the feeling from your last paragraph “… in 5-10 years…” that you expect answers now. Simple, straight-forward answers. Sorry, but the world doesn’t work that way. Nobody is going to come around and say “this one thing is the cause of autism” — in part, because we aren’t even sure that “autism” is really one thing itself. It could be a whole bunch of things with similar symptoms and different causes.

    People have a strong desire for simple answers. This is why the woo-meisters can peddle “vitamin deficiency is the cause of every disease known” or liver flukes or blocked colons. Simple answers. But the universe isn’t simple. The human body isn’t simple. Simple answers don’t often work.

  86. #87 Dr Aust
    June 19, 2010

    Re. the UK “Audience with Andrew Wakefield” (see comment #82), there is a thread over on the Bad Science Forum which gives the as-it-happened story of this ill-starred event.

    Apparently when someone told the TV Company precisely who had booked their rehearsal studio they cancelled the booking, and the whole thing had to take place in a hastily-organised pub/hotel function room with about a dozen people there. Though doubtless that will just feed the paranoid GroupThink at the various national affiliates of Vaccine Conspiracy Inc (Chief “Scientific” Adviser: Mr A Wakefield).

  87. #88 Sauceress
    June 19, 2010

    Dr Aust
    Just read through that thread over at Bad Science. Unsurprising then that AoA is currently touting this headline:

    Radio Wakefield Up Now on “Pirate Satellite”! Chased From Venue to New Locale!

    Add this comment by Journal Checker over at Bad Science..

    Not surprising then that the video with Polly Tommey claiming “threats” has been removed from the internet. Maybe someone has a recording?

    Their dishonesty of desperation is strong in this latest little manufactroversy!

  88. #89 Chris
    June 19, 2010

    Reading the new thread on why they had to change venues at:
    http://www.badscience.net/forum/viewtopic.php?f=3&t=16796&start=75

    Quoting from there:

    Next morning, at about 9am I received emails from two directors saying that their rehearsal studio had been booked via a third party who was known to them, but the person who took the booking was not informed of the nature of the event, nor of the links to Wakefield and the anti-vax lobby. They withdrew the offer of the room.

  89. #90 Brian Deer
    June 20, 2010

    I have to say, the Wakefield event in London gave me one of those “oh, I never expected that to happen” Bin Laden moments. His support has simply imploded, collapsed. Every indicator shows this: sales of his fiction, website visits, attendees at events. It’s kind of pitiful really. Apart from Mr Stone, Betty Bonkers (as Isabella Thomas is known to her friends) and most of the usual suspects among the crooks, cranks and quacks who’ve circled the wagons around this charlatan, nobody came.

    Meanwhile, I had four times as many people come to hear my most engrossing and entertaining Powerpoint epistle on Wakefield – “Research Fraud for Dummies” – at a skeptics in the pub meeting in Leicester. Maybe I should show it at the next DAN!/Autism One/Quacks in the Park thing.

  90. #91 David N. Andrews M. Ed., C. P. S. E.
    June 27, 2010

    @Orac: “I’d be happy to educate him.”

    Do you really think it’d be successful? I mean – really? He’s from the same camp as the rest of those AoA idiots whose brains are mostly limbic system (about 90% hippocampal/amygdaloidal tissue, about 10% urine and practically bugger-all cerebral tissue). Chances of educating someone like that are low: all you’ll get for your pains is a deputation from that crowd surfacing over here, getting all emotionally upset with you and then pissing themselves because of that all over the blog… You really want that?

    Nah. Didn’t think so.