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OSR#1

30 Jun

My own contribution is here, with less science and more snark:

Please leave your comments there or here, it doesn’t matter.

In support of David Gorski

22 Jun

To whomever it may concern,

You have probably recently had to deal with a handful of vitriolic comments regarding the online activities of David Gorski. You will probably have been pointed to an online essay by a young man called Jake Crosby in which he makes a series of claims regarding David Gorski and his ‘ties’ to vaccines/vaccine manufacturers and other entities.

I urge you to read these comments and this essay very, very carefully. Once you do I am in no doubt that you will see what the rest of us clearly can – that this work is the work of a highly impassioned young man who believes that he is right. He believes that vaccines cause autism to state it clearly and he believes that by having some kind of – any kind of – tie to a pharma organisation means that David Gorski is ‘tainted’. But what really annoys master Crosby is the fact that David Gorski regularly blogs in support of the science that clearly shows vaccines do not cause autism and blogs against the pseudo science that attempts – and continually fails- to draw any kind of a link between vaccines and autism.

So this, in master Crosby’s eyes, is David Gorski’s crime – supporting the science and decrying the bad science.

In order to cast some kind of suspicion over David Gorski’s support of science, Crosby has ‘discovered’ that Gorski is conducting research into ways to reuse some types of drugs – drugs developed by Sanofi-Aventis who of course also manufacture some vaccines. And that, despite another few hundred words from master Crosby is that. That is the sum total of his ‘investigation’ and the sum total of David Gorski’s crime.

The only real eye-opener on this issue is that Jake Crosby managed to wring out as many words as he did on this total non-issue.

I have known David Gorski online for a number of years. We often quote one another and link to one anothers posts. We regularly email each other and I was disappointed to be unable to meet him for drinks on a visit to the UK he took a few years ago. In my experience of the man he is rigorous, almost fanatical with regards to accuracy and brings these traits to many areas of blogging and online writing including the investigation of bad science.

Why does it matter to me? It matters because I have an autistic child and an autistic step child. When my autistic child was first diagnosed I firmly believed that her autism was caused by vaccines. It was only through being exposed to writings of David Gorski and his peers on the science of autism and the bad science of the autism/vaccine connection that I eventually saw for myself what was obvious: vaccines don’t cause autism and never did.

Scientists such as David Gorski often blog and write online anonymously. They do this because to be exposed to the sort of people Jake Crosby colludes with often means being exposed to harassment and threats. David Gorski is now finding that out for himself. I hope that you as his peers, colleagues and employers will see how vital it is that David Gorski continues blogging and that you will support him in both his work and his blogging.

Interview with Stephen Scherer

11 Jun

Stephen Scherer is co-author on the recent paper ‘Functional impact of global rare copy number variation in autism spectrum disorders‘. I caught up with him via email to ask a few questions:

1) What is the ‘bottom line’ message readers can take away from your work?

I am always frustrated when I hear at the end of most news stories…’and we don’t know what can cause autism’. Data from the past few years including our new study show alterations in genes can cause autism. We have not found all of the genes yet, and not all autism cases can be accounted for (the genetics can be complex) but genes can cause autism. For the specialists, through our new study we show either de novo or rare inherited copy number variations as one form of genetic alteration involved in autism. The genes affected are often linked together in a connected functional pathway and may of these molecules dictate how brain cells (neurons) develop and communicate. Some of the autism genes we found have already been found to cause intellectual disabilities, which is not entirely surprising since many individuals with autism also have these challenges.

2) How does your paper tie in with other gene/autism studies?

We validate many previous findings, but also find dozens and dozens of new autism risk genes. Our data furthers the hypothesis that rare genetic alterations contribute much more relative risk to developing autism than common genetic variations.

3) What should future researchers use your study for in terms of direction to take their own work?

I think one of the most important impacts of the study is the design itself. Nature really wanted us to include the Figure 1, which outlines the design and analysis. CNV studies are still quite tricky to do and the data has to be of the highest quality to make sense of it. I think our study on autism will set the standard for all other studies going forward, so they should follow it. Moreover, many of the functional pathway studies published before may have been either underpowered, flawed by low resolution arrays or high false discovery rates, or incomplete study designs. We spent alot of time thinking of how to best do this properly so if others are interested they should read the Supplementary Information carefully. Use it as a guide. Finally, for the functional biologists look at the long list of genes we present in the Supplementary Information since they may find their favorite gene to be an autism candidate gene!

4) How difficult was it managing the input from such a very large amount of co-authors?

The Autism Genome Project has some 120 scientists from 11 countries involved (see the authorship list). We selected a ‘writing team’ comprised of genome scientists, statisticians, medical geneticists, psychiatrists and developmental pediatricians. Interesting, everyone saw their own story in the data. I pretty much new in advance what I wanted to see in the final manuscript so much of my job was bring focus to the many other good ideas (note that there are five other papers spinning out of this larger study presenting some of these other data and interpretations). In took about 12 solid months of analysis of the data, three months of writing and editing, alot of cursing, and then submission to Nature (with even more cursing). The review time from submission to publication took ~six months. This was the hardest for me (except other than constantly changing the author list….and affiliations). The reviewers were very very thorough and Nature can (rightfully) be very demanding. In the end we are very proud of the manuscript. Dalila Pinto who is the first author and a post-doc in the lab was the driving force behind the analysis and deserved a lions-share of the credit. Would I do it again? I’ve had two Senior Author papers in Nature this year, which have been very draining. But I would do it again!

The Thinking Person’s Guide to Autism

7 Jun

There’s a new blog/book project in town and its right here (or @thinkingautism on Twitter or here on Facebook).

The Thinking Person’s Guide to Autism (TPGA) is the book and website we wish had been available when our children with autism were first diagnosed.

…

Think of us as a little bit of Snopes for the autism community — trusted, accurate, and friendly. Our essays will cover informed approaches to autism and autism treatments, as well as the personal experiences of people with autism and their families.

There’s a great team of people behind this project and I for one am greatly looking forward to the content they put out.

Urine test for autism? Hmmm

4 Jun

Following on from Lisa Jo’s well placed concerns about this study,I also have a few. Namely the references. Not being scientifically qualified to tackle the meat of the paper I look straight at what the researcher uses to support his ideas. So far I’ve found these references the authors base their paper on:

1) Kidd, P. M. Autism, an extreme challenge to integrative medicine. Part: 1: The knowledge base. Altern. Med. Rev. 2002, 7 (4), 292–316.

2) Ashwood, P.; Anthony, A.; Pellicer, A. A.; Torrente, F.; Walker-Smith, J. A.; Wakefield, A. J. Intestinal lymphocyte populations in children with regressive autism: evidence for extensive mucosal immunopathology. J. Clin. Immunol. 2003, 23 (6), 504–17.

3) Bolte, E. R. Autism and Clostridium tetani. Med. Hypotheses 1998, 51 (2), 133–44

4) James, S. J.; Cutler, P.; Melnyk, S.; Jernigan, S.; Janak, L.; Gaylor, D. W.; Neubrander, J. A. Metabolic biomarkers of increased oxidative stress and impaired methylation capacity in children with autism. Am. J. Clin. Nutr. 2004, 80 (6), 1611–7

At the very least, relying on studies from Alternative Medical Review, studies co-authored by Andrew Wakefield, studies from Medical Hypothesis and studies co-authored by Jim Neubrander should give rise to questions over the credibility of this paper. Is it enough to scupper it? Of course not. But when we take Lisa Jo’s questions into the bargain – that autism does not always, if ever, have a distinct GI component, I have to wonder about this paper.

Addressing the ‘too many too soon’ hypothesis

3 Jun

Regular readers may be aware that I blogged about a study recently that demonstrated the early stages of tackling the ‘too many too soon’ hypothesis. It came in for some fierce criticism in the comment section so I wrote to the lead author to get his thoughts. What follows is his answer to me via email:

Reviewing your blog, there are two related criticisms of our study.

First, I must clarify the conflict of interest comment. Though less relevant in my mind, it addresses the other limitations noted by your readers. This study was completely unfunded – not by any pharmaceutical company, not by the CDC. We did this all in our free time because of a simple non-financial “conflict” – as infectious disease physicians we take care of children who suffer needlessly from vaccine preventable diseases. This clarification of funding leads to point 2 – because we
did not have millions of dollars at our disposal we chose to use pre-existing data to address a common parental concern for which we could not find any evidence-based talking points.

This strategy had significant benefits – once we had the idea for this study we got right to work and did not have to wait 7-10 years to see what the outcomes might be. However, as we acknowledge in the discussion (and your readers point out), the use of pre-existing data also introduces limitations. We did not have control over which outcomes were tested, nor which children were included or excluded from the original study.

Nevertheless, I believe this study was accepted for publication in an academic medical journal because it offers a unique methodology that may be used to study the effects of delayed vaccination on any outcome of choice, whether it be the incidence of vaccine-preventable diseases or the proposed vaccine side effect du jour. Unfortunately, I do not have the resources to perform these studies myself.

A separate question – which is really a critique of the original NEJM study (with which I was not involved) and not ours per se – is why the authors chose to exclude the children they did. In the time since you e-mailed be I believe “Luna_the_cat” has explained this fairly clearly. Basically, the original study excluded children with brain injuries that would not have been related to vaccination (except for a few – pneumococcal and haemophilus influenza meningitis which vaccines PREVENT) and this seemed reasonable in the initial study. Furthermore, the majority of these exclusion criteria are prenatal or congenital diagnoses that would have predated vaccination anyway.

Finally, regarding lack of “controls”. This was not a “vaccinated versus unvaccinated” study, nor was it intended to be. It was designed to address the “too many too soon” hypothesis. Our “controls” were those children in the cohort who received fewer vaccines later during the first year of life. In this case the “exposure” was timely vaccine receipt – which was never associated with any adverse neurodevelopmental outcomes.

Blocking immunisation

2 Jun

The rise of a public anti-vaccine movement in the US is partly to blame for blocking effective immunisations according to the AAP today.

A story on WebMD says that the

…rise of a public anti-vaccination movement that uses the Internet as well as standard media outlets to promote its position, which is “wholly unsupported by any scientific evidence” linking vaccines with autism and other childhood conditions.

is at least partly to blame for ensuring that ‘pockets’ of unimmunised children exist throughout the US. Other reasons given include problems with cost.

Read the whole story at Web MD (@WebMd).

Andrew Wakefield – as succesful an author as researcher

2 Jun

Andrew Wakefields supporters were hoping his new book would be a bestseller. That ain’t going to happen given how much a publishing insider revealed to me how many he has actually sold:

He sold a total of 1017 copies. Top sales 157 copies in NYC. 46 in LA, 43 in Atlanta (perhaps CDC people wanted to see what he said?!), 38 in Boston, 24 in Chicago, 18 in Seatlle and 17 copies in his hometown of Austin

Ouch. It’ll be interesting to see how well the book does as interest in it fades. Or maybe ‘well’ isn’t the right word.

Autism and mental retardation – genetic overlap

30 May

Post taken from Medical News Today

Researchers working with Professor Gudrun Rappold, Director of the Department of Molecular Human Genetics at Heidelberg University Hospital, have discovered previously unknown mutations in autistic and mentally impaired patients in what is known as the SHANK2 gene, a gene that is partially responsible for linking nerve cells. However, a single gene mutation is not always enough to trigger the illness. In some cases, a certain threshold of mutation must be exceeded. The researchers conclude from their results that a correct inner structure of the nerve cell synapses is necessary to enable the normal development of language, social competence, and cognitive capacity. Essential for the success of the project were the studies by the Heidelberg research team with the doctoral student Simone Berkel and collaboration with a Canadian research team headed by Steve Scherer. The study has already been published online in the leading scientific journal Nature Genetics.

Autism is a congenital perception and information-processing disorder of the brain that is often associated with low intelligence, but also with above-average intelligence. The disease is characterized by limited social communication and stereotypical or ritualized behavior. Men are affected much more frequently than women. Autism and mental retardation can occur together but also independently of one another and are determined to a great extent by hereditary factors. Some of the responsible genes have already been identified but the precise genetic mechanisms have not yet been explained.

Genetic makeup of hundreds of patients analyzed

Professor Rappold and her team focused their studies on the SHANK2 gene, which encodes a structural protein at the nerve cell synapses. It is responsible for the mesh structure of the basic substance in the postsynapse. Only when the postsynapse is properly structured can nerve impulses be correctly transmitted. The researchers analyzed the genetic material of a total of 396 patients with autism and 184 patients with mental retardation. They found different mutations in their SHANK2 genes in the area of individual base pairs, but also variants in the number of gene copies. The mutations led to varying degrees of symptoms. None of the observed gene variants occurred in healthy control persons. “Apparently an intact postsynaptic structure is especially important for the development of cognitive functions, language, and social competence,” explained Professor Rappold.

Identical mutations as the cause of different diseases

Some of the genetic mutations identified were new occurrences of mutations that were not inherited from the parents, but some of the mutations were also found in one parent. Since there are also healthy carriers of gene variants, we must assume that a certain threshold of gene mutations must be exceeded for the disease to appear. “Moreover, the same mutation can be present in an autistic patient with normal intelligence and in a mentally impaired patient,” said Professor Rappold. There is some overlap in the clinical symptoms of mental retardation and autism, which can now be explained by a common genetic cause.

The American Rally for Personal Rights – bit of a damp squib

27 May

Yesterday was the American Rally for Personal Rights (an anti-vaccine rally) held between 3pm and 5pm in a park in Chicago, US. In attendance was ex-doctor Andrew Wakefield in whose honour the rally was held.

Hoping for thousands, the organisers got what looks like a hundred or so (click for full size).

including one young man (A certain J. Crosby, Age of Autism Editor) who carried the sign ‘Autistics for Wakefield’

I’m not entirely certain who the autistics were. I mean I see Jake but no one else. Also in attendance were Wade Rankin, Erik Nanstiel, Boyd Haley, Bob Krakow and Jim Moody and for ‘name’ anti-vaxxers that was it. No Jenny McCarthy, No Jim Carrey, No Generation Rescue, No Age of Autism bigwigs (aside from young master Crosby of course).

Of course for bloggers such as I, this is a tad disappointing. There’s not really a lot to talk about when nothing much happens, nobody of any consequence shows up and the whole thing resembles a rain-soaked firecracker.

On the bright side, there were The Refusers who I’m pretty sure would’ve been good for a very hearty laugh. Aside from that – nothing really to tell. The sun was out, some anti-vaxxers waved a few signs around and the world collectively yawned.

See ANB’s take on it, he actually attended the rally himself.

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