critiquing another thesis on vaccination

Given the fuss occasioned by her PhD thesis, I was interested to look at the document produced for Judy Wilyman's MSc (available here on-line), largely to see what attention had been given to the science content and perspectives. Having examined or adjudicated a number of Masters theses in the sciences, I've a reasonably good idea of the standards of scholarship and scientific knowledge expected from this level of graduate research.

The section around research questions is interesting, in that it describes the purpose of the research project as

to provide supportive evidence for the Australian Government’s Pertussis Immunisation Policy.

This sounds a little like an a priori argument; I'd have expected something more like "to assess the evidence for…" (although one would have hoped that the Australian Government had assessed the evidence itself before implementing its policy). The author goes on to say (p.7) that

Vaccination is a medical intervention that introduces a suspension of live (attenuated) or inactivated microorganisms and chemical substances into a healthy body to induce immunity to a particular disease (Stern A. and Markel H, 2005).

The article by Stern & Markel actually identifies more than just live or inactivated micro-organisms as being used to elicit an immune response. As also noted here, the antigenic component of vaccines (the part that elicits an immune response) may be of four types: 'live attenuated', 'inactivated' (where the microbe has been killed), 'sub-unit' (ie only an antigenic protein or other molecule is used; there is no actual bacterium or virus present), and 'toxoid' (inactivated form of a toxin produced by the microbe). It's clear that Wilyman is not talking about the latter two in her description of vaccination, as she then lists the 'chemical substances' as

preservatives, antibiotics and adjuvants that are contained in a vaccine carrier.

She goes on to say (p.8) that

Therefore it is important to consider the cumulative and synergistic effects of chemicals in vaccines and any other drugs taken at the same time. This policy applies to all individuals so consideration should also be given to the knowledge that exists on genetic factors that predispose some children to greater risks. This risk must be weighed against an accurate knowledge of the chances of harm being caused by the disease itself.

On the surface this sounds reasonable. I'd therefore expect, in an MSc thesis, a section setting out the current state of knowledge about the workings of the immune system, a brief explanation of how vaccine safety is assessed, and data on morbidity and mortality associated with pertussis (the Vaccine-Preventable Disease, VPD, that is the subject of the thesis).

So it was disconcerting to find that at least some references are rather outdated. The discussion of immunity, for example, appears to be based on a textbook published in 1952. This is unusual, given the advances in our understanding that have occurred in the intervening 60+ years. This is also true for the source of a statement (citation published in 1956) that VPDs are no longer a cause of infant mortality.

No-one disputes that hygiene and living standards play a significant role in enhancing public health, but the current scientific consensus is that vaccines also play a significant role in reducing both mortality and morbidity related to VPDs. The data presented here are quite instructive in that regard: while they are from the US there is no good reason to expect that the Australian situation is different. Not only deaths, but also rates of significant illness, fell with the introduction of vaccines for the various VPDs. Chapter 3 of the thesis includes only mortality data, although the author also notes in an earlier section (p.11) that

Complications or morbidity from pertussis disease include:  1) Pneumonia – resulting from B.pertussis itself or secondary infections. 2) Atelectasis – a failure of part of the lung to expand due to mucus plugs. 3) Otitis media and sinusitis are common and usually due to S.pneumoniae.  4) Ruptured alveoli and emphysema. 5) Bronchiectasis – widening of the bronchi in which pus forms. 6) Convulsions and encephalopathy (Behrman et al, 1998).  

Wilyman goes on to say that

Celermajer J, and Brown J, (1966) studied the morbidity due to pertussis over an eleven year period from 1953 – 1964 and concluded pertussis in the Sydney community appears to be only infrequently associated with neurological complications and these tend to be mild in nature.

This does rather gloss over all the other forms of morbidity identified above, and raises some concerns about special pleading. In addition, there is again some concern around the date of the reference; is this statement supported by more recent reviews of the data (the thesis was submitted in 2007)?

In that regard it's also notable that discussion around the waning of immunity provided by the whole-cell pertussis vaccine clouds the waters a little as this vaccine was removed from use in Australia in the 2000s, to be replaced by an acellular vaccine containing key antigens. It's never been a live-cell vaccine, so the comment about reversion to virulence (p.39) is a little odd. (There's some really interesting science in the linked article, which discusses research findings examining the possibility that the pertussis bacterium may have evolved in such a way that some strains no longer express one of the key antigens in the vaccine. This means that the vaccine may be less effective in eliciting an appropriate immune response; however, it seems this may possibly be offset by a loss of the bacterium's ability to cause severe disease, and overall the study found pertussis vaccination to be effective.)

Incidentally, the scientific and medical communities agree that no vaccination is 100% effective; around 70-90% of those receiving the pertussis vaccine acquire full immunity. However, it is an interesting use of stats to suggest (p. 40) that because approximately 1/3 of children presenting with pertussis to one hospital in 1964 were fully vaccinated, that 1/3 of the fully-vaccinated cohort will still get the disease. There is a good analysis of this concept here.

At this point I began to feel that the approach taken in the thesis was intended less to provide 'supportive evidence' and more to develop arguments against the use of vaccines. For that reason I skipped ahead to the Conclusions section, because this is often a very informative section of any thesis, where the author's findings and recommendations are to found.

I'm afraid that this section really did confirm my developing impression. Here is one paragraph (p.69), broken down to include my own comments.

Prior to the implementation of mass vaccination programs, Burnet M, (1952) indicated that there were many gaps in scientist’s knowledge about the functioning of the human immune system. 

Fifty years on it is known that vaccination doesn’t provide lasting immunity

 and a ‘modified infection’ means bacteria or virus’s that are treated with preservatives, antibiotics and stabilizers that parents are not informed about. 

These chemicals are known allergens and neurotoxins such as mercury, formaldehyde and aluminium. 

In the twenty-first century the effects of these chemicals on biological cells are well known 

and parents are trying to avoid them in their children’s diet. Yet parents are not being told they are injecting them into their babies bodies at the most vulnerable stage in their development.