MedDRA + VAERS: A marriage made in hell?

This post is a Golden DDoS Award winner

So far, this blog was DDoS’d only three times within 24 hours of its publication. That deserves a prize.

Quick: what do a broken femur, Henoch-Schönlein purpura, fainting, an expired vaccine and a healthy childbirth have in common? If your answer was “they’re all valid MedDRA codes”, you’re doing pretty well. If you, from that, deduced that they all can be logged on VAERS as adverse effects of vaccination, you’re exceeding expectations. And if you also realise that the idea that Jane got an expired HPV vaccine, and as a consequence broke her femur, developed Henoch-Schönlein purpura, and suddenly gave birth to a healthy baby boy is completely idiotic and yet can be logged on VAERS, you’re getting where I’m going.

MedDRA is a medical nomenclature specifically developed for the purposes of pharmacovigilance. The idea is, actually, not dreadful – there are some things in a usual medical nomenclature like ICD-10 that are not appropriate for a nomenclature used for pharmacovigilance reporting (V97.33: sucked into jet engine comes to my mind), and then there are things that are specific to pharmacovigilance, such as “oh shoot, that was not supposed to go up his bum!” (MedDRA 10013659: vaccine administered at inappropriate site), “we overdosed little Johnny on the flu vaccine!” (MedDRA 10000381: drug overdose, accidental) and other joys that generally do only happen in the context of pharmacovigilance. So far, so good.

At the same time, MedDRA is non-hierarchical, at least on the coding level. Thus, while the ICD code V97.33 tells you that you’re dealing with an external cause of mortality and morbidity (V and Y codes), specifically air and space transport (V95-97), more specifically ‘other’ specific air transport accidents, specifically getting sucked into a jet engine (V97.33), there’s no way to extract from MedDRA 10000381 what the hell we’re dealing with. Not only do we not know if it’s a test result, a procedure, a test or a disease, we are hopelessly lost as to figuring out what larger categories it belongs to. To make matters worse, MedDRA is proprietary – which in and of itself is offensive to the extreme to the idea of open research on VAERS and other public databases: a public database should not rely on proprietary encoding! -, and it lacks the inherent logic of ICD-10. Consider the encoding of the clinical diagnosis of unilateral headache in both:

SOC: System Organ Class, HLGT: High Level Group Term, HLT: High Level Term, PT: Preferred Term, LLT: Lower Level Term

Attempting to encode the same concept in MedDRA and ICD-10, note that the final code in MedDRA (10067040) does not allow for the predecessors to be reverse engineered, unless a look-up table is used – which is proprietary. ICD-10, at the same time, uses a structure that encodes the entire ‘ancestry’ of an entity in the final code. Not only does this allow for intermediate codes, e.g. G44 for an ‘other’ headache syndrome until it is closer defined, it also allows for structured analysis of the final code and even without a look-up table (which is public, as is the whole ICD-10), the level of kinship between two IDC-10 codes can be ascertained with ease.

We know that an ICD code beginning with F will be something psychiatric and G will be neurological, and from that alone we can get some easy analytical approaches (a popular one is looking at billed codes and drilling down by hierarchical level of ICD-10 codes, something in which the ICD-10 is vastly superior to its predecessor). MedDRA, alas, does not help us such.

Garbage in, garbage out

OK, so we’ve got a nomenclature where the codes for needlestick injury, death, pneumonia, congenital myopathy and a CBC look all the same. That’s already bad enough. It gets worse when you can enter any and all of these into the one single field. Meet VAERS.

The idea of VAERS is to allow physicians, non-physicians and ‘members of the public’ to report incidents. These are then coded by the CDC and depending on seriousness, they may or may not be investigated (all reports that are regarded as ‘serious’ are investigated, according to the CDC). The problem is that this approach is susceptible to three particular vulnerabilities:

  • The single field problem: VAERS has a single field for ‘symptoms’. Everything’s a symptom. This includes pre-existing conditions, new onset conditions, vaccination errors, lab tests (not merely results, just the tests themselves!), interventions (without specifying if they’re before or after the vaccine), and so on. There is also no way to filter out factors that definitely have nothing to do with the vaccine, such as a pre-existing birth defect. The History/Allergies field is not coded.
  • The coding problem: what gets coded and what does not is sometimes imperfect. This being a human process, it’s impossible to expect perfection, but the ramifications to this to certain methods of analysis are immense. For instance. if there are 100 cases of uncontrollable vomiting, that may be a signal. But if half of those are coded as ‘gastrointestinal disorder’ (also an existing code), you have two values of 50, neither of which may end up being a signal.
  • The issue of multiple coding: because MedDRA is non-hierarchical, it is not possible to normalise at a higher level (say, with ICD-10 codes, at chapter or block level), and it is not clear if two codes are hierarchically related. In ICD-10, if a record contains I07 (rheumatic tricuspid valve disease) and I07.2 (tricuspid stenosis with tricuspid insufficiency), one can decide to retain the more specific or the less specific entry, depending on intended purpose of the analysis.

In the following, I will demonstrate each of these based on randomly selected reports from VAERS.

The Single Field Problem (SFP)

The core of the SFP is that there is only one codeable field, ‘symptoms’.

VAERS ID 375693-1 involves a report, in which the patient claims she developed, between the first and second round of Gardasil,

severe stomach pain, cramping, and burning that lasted weeks. Muscle aches and overall feeling of not being well. In August 2009 patient had flu like symptoms, anxiety, depression, fatigue, ulcers, acne, overall feeling of illness or impending death.

Below is the patient’s symptom transposition into MedDRA entities (under Symptoms):

Event details for VAERS report 375693-1

The above example shows the mixture of symptoms, diagnostic procedures and diagnostic entities that are coded in the ‘Symptoms’ field. The principal problem with this is that when considering mass correlations (all drugs vs all symptoms, for instance), this system would treat a blood test just as much as a contributor to a safety signal as anxiety or myalgia, which might be true issues, or depression, which is a true diagnosis. Unfiltered, this makes VAERS effectively useless for market basket analysis based (cooccurrence frequency) analyses.

Consider for instance, that PRR is calculated as

PRR_{V,R} = \frac{\Sigma (R \mid V) \/ \Sigma (V)}{\Sigma (R \mid \neg V) \/ \Sigma (\neg V)} = \frac{\Sigma (R \mid V)}{\Sigma (V)} \cdot \frac{\Sigma (\neg V)}{\Sigma (R \mid \neg V)}

where V denotes the vaccine of interest, R denotes the reaction of interest, and the \Sigma operator denotes the sum of rows or columns that fulfill the requisite criteria (a more detailed, matrix-based version of this equation is presented here). But if \{R\}, the set of all R, contains not merely diagnoses but also various ‘non-diagnoses’, the PRR calculation will be distorted. For constant V and an unduly large R, the values computationally obtained from the VAERS data that ought to be \Sigma(R \mid V) and \Sigma(R \mid \neg V) will both be inaccurately inflated. This will yield inaccurate final results.

Just how bad IS this problem? About 30% bad, if not more. A manual tagging of the top 1,000 symptoms (by N, i.e. by the number of occurrences) was used as an estimate for how many of the diagnostic entities do not disclose an actual problem with the vaccine.

In this exercise, each of the top 1,000 diagnostic codes (by N, i.e. by occurrence) were categorised into a number of categories, which in turn were divided into includable (yellow) and non-includable (blue) categories. An includable category reveals a relevant (=adverse) test result, a symptom, a diagnosis or a particular issue, while non-includables pertain to procedures, diagnostics without results, negative test results and administration, storage & handling defects.

According to the survey of the top 1,000 codes, only a little more than 70% of the codes themselves disclose a relevant issue with the vaccine. In other words, almost a third of disclosed symptoms must be pruned, and these cannot be categorically pruned because unlike ICD-10, MedDRA does not disclose hierarchies based on which such pruning would be possible. As far as the use of MedDRA goes, this alone should be a complete disaster.

Again, for effect: a third of the codes do not disclose an actual side effect of the medication. These are not separate or identifiable in any way other than manually classifying them and seeing whether they disclose an actual side effect or just an ancillary issue. Pharmacovigilance relies on accurate source data, and VAERS is not set up, with its current use of MedDRA, to deliver that.

The coding problem

Once a VAERS report is received, it is MedDRA coded at the CDC. Now, no manual coding is perfect, but that’s not the point here. The problem is that a MedDRA code does not, in and of itself,  indicate the level of detail it holds. For instance, 10025169 and 10021881 look all alike, where in fact the first is a lowest-level entity (an LLT – Lower-Level Term – in MedDRA lingo) representing Lyme disease, while the former is the top-level class (SOC – System Organ Class) corresponding to infectious diseases. What this means is that once we see a MedDRA coded entity as its code, we don’t know what level of specificity we are dealing with.

The problem gets worse with named entities. You see, MedDRA has a ‘leaf’ structure: every branch must terminate in one or more (usually one) LLT. Often enough, LLTs have the same name as their parent PT, so you get PT Lyme disease and LLT Lyme disease. Not that it terrifically matters for most applications, but when you see only the verbose output, as is the case in VAERS, you don’t know if this is a PT, an LLT, or, God forbid, a higher level concept with a similar name.

Finally, to put the cherry on top of the cake, where a PT is also the LLT, they have the same code. So for Lyme disease, the PT and LLT both have the code 10025169. I’m sure this seemed like a good idea at the time.

The issue of multiple coding

As this has been touched upon previously, because MedDRA lacks an inherent hierarchy, a code cannot be converted into its next upper level without using a lookup table, whereas with, say, ICD-10, one can simply normalise to the chapter and block (the ‘part left of the dot’). More problematically, however, the same code may be a PT or an LLT, as is the case for Lyme disease (10025169).

Let’s look at this formally. Let the operator \in^* denote membership under the transitive closure of the set membership relation, so that

  1. if x \in A, then x \in^* A,
  2. if x \in A and A \subseteq B, then x \in^* B.

and so on, recursively, ad infinitum. Let furthermore \in^*_{m} denote the depth of recursion, so that

  1. for x \in A:  x \in^*_{0} A,
  2. for x \in A \mid A \subseteq B:  x \in^*_{1} B,

and, once again, so on, recursively, ad infinitum.

Then let a coding scheme \{S_{1...n}\} exhibit the Definite Degree of Transitiveness (DDoT) property iff (if and only if) for any S_m \mid m \leq n, there exists exactly one p for which it is true that S_m \in^*_{p} S.

Or, in other words, two codes S_q, S_r \mid q, r \leq n, may not be representable identically if p_q \neq p_r. Less formally: two codes on different levels may not be identical. This is clearly violated in MedDRA, as the example below shows.

Violating the Definite Degree of Transitiveness (DDoT) property: PT Botulism and LLT Botulism have different p numbers, i.e. different levels, but have nonetheless the same code. This makes the entity 10006041 indeterminate – is it the PT or the LLT for botulism? This is a result of the ‘leaf node constraint’ of MedDRA’s design, but a bug by design is still a bug, not a feature.

Bonus: the ethical problem

To me as a public health researcher, there is a huge ethical problem with the use of MedDRA in VAERS. I believe very strongly in open data and in the openness of biomedical information. I’m not alone: for better or worse, the wealth – terabytes upon terabytes – of biomedical data, genetics, X-ray crystallography, models, sequences  prove that if I’m a dreamer, I’m not the only one.

Which is why it’s little short of an insult to the public that a pharmacovigilance system is using a proprietary encoding model.

Downloads from VAERS, of course, provide the verbose names of the conditions or symptoms, but not what hierarchical level they are, nor what structure they are on. For that, unless you are a regulatory authority or a ‘non-profit’ or ‘non-commercial’ (which would already exclude a blogger who unlike me has ads on their blog to pay for hosting, or indeed most individual researchers, who by their nature could not provide the documentation to prove they aren’t making any money), you have to shell out some serious money.

MedDRA is one expensive toy.

Worse, the ‘non-profit’ definition does not include a non-profit research institution or an individual non-profit researcher, or any of the research bodies that are not medical libraries or affiliated with educational institutions but are funded by third party non-profit funding:

This just keeps getting worse. Where would a non-profit, non-patient care provider, non-educational, grant-funded research institution go?

There is something rotten with the use of MedDRA, and it’s not just how unsuitable it is for the purpose, it is also the sheer obscenity of a public database of grave public interest being tied to a (vastly unsuitable and flawed, as I hope it has been demonstrated above) nomenclature.

Is VAERS lost?

Resolving the MedDRA issue

Unlike quite a few people in the field, I don’t think VAERS is hopelessly lost. There’s, in fact, great potential in it. But the way it integrates with MedDRA has to be changed. This is both a moral point – a point of commitment to opening up government information – and one of facilitating research.

There are two alternatives at this point for the CDC.

  1. MedDRA has to open up at least the 17% of codes, complete with hierarchy, that are used within VAERS. These should be accessible, complete with the hierarchy, within VAERS, including the CDC WONDER interface.
  2. The CDC has to switch to a more suitable system. ICD-10 alone is not necessarily the best solution, and there are few alternatives, which puts MedDRA into a monopoly position that it seems to mercilessly exploit at the time. This can – and should – change.

Moving past the Single Field Problem

MedDRA apart, it is crucial for VAERS to resolve the Single Field Problem. It is clear that from the issues presented in the first paragraph – a broken femur, Henoch-Schönlein purpura, fainting, an expired vaccine and a healthy childbirth – that there is a range of issues that need to be logged. A good structure would be

  1. pre-existing conditions and risk factors,
  2. symptoms that arose within 6 hours of administration,
  3. symptoms that arose within 48 hours of administration,
  4. symptoms that arose later than 48 hours of administration,
  5. non-symptoms,
  6. clinical tests without results,
  7. clinical tests segmented by positive and negative results, and
  8. ancillary circumstances, esp. circumstances pertaining to vaccination errors such as wrong vaccine administered, expired vaccine, etc.

The use of this segmentation would be able to differentiate not only time of occurrence, but also allow for adequate filtering to identify the correct denominators for the PRR.

A future with (for?) MedDRA

As said, I am not necessarily hostile to MedDRA, even if the closet libertarian in me bristles at the fact that MedDRA is mercilessly exploiting what is an effective monopoly position. But MedDRA can be better, and needs to be better – if not for its own economic interests, then for the interests of those it serves. There are three particular suggestions MedDRA needs to seriously consider.

  1. MedDRA’s entity structure is valuable – arguably, it’s the value in the entire project. If coding can be structured to reflect its internal hierarchy, MedDRA becomes parseable without a LUT,[1] and kinship structures become parseable without the extra step of a LUT.
  2. MedDRA needs to open up, especially to researchers not falling within its narrowly defined confines of access. Especially given the inherent public nature of its use – PhV and regulation are quintessentially public functions, and this needs an open system.
  3. MedDRA’s entity structure’s biggest strength is that it comprises a range of different things, from administrative errors through physical injuries to test results and the simple fact of tests.


VAERS is a valuable system with a range of flaws. All of them are avoidable and correctable – but would require the requisite level of will and commitment – both on CDC’s side and that of MedDRA. For any progress in this field, it is imperative that the CDC understand that a public resource maintained in the public interest cannot be driven by a proprietary nomenclature, least of all one that is priced out of the range of the average interested individual: and if they cannot be served, does the entire system even fulfill its governmental function of being of the people and for the people? It is ultimately CDC’s asset, and it has a unique chance to leverage its position to ensure that at least as far as the 17% of MedDRA codes go that are used in VAERS, these are released openly.

In the end, however sophisticated our dissimilarity metrics, when 30% of all entities are non-symptoms and we need to manually prune the key terms to avoid denominator bloat due to non-symptom entities, such as diagnostic tests without results or clearly unconnected causes of morbidity and mortality like motor vehicle accidents, dissimilarity based approaches will suffer from serious flaws. In the absence of detailed administration and symptom tracking at an individual or institutional level, dissimilarity metrics are the cheapest and most feasible ways of creating value out of post marketing passive reports. If VAERS is to be a useful research tool, as I firmly believe it was intended to be, it must evolve to that capability for all.

References   [ + ]

1. Look-up table

SafeGram: visualising drug safety

Update: an RMarkdown notebook explaining the whole process is available here.

Visualising vaccine safety is hard. Doing so from passive (or, as we say it in Britain, ‘spontaneous’!) pharmacovigilance (PhV) sources is even harder. Unlike in active or trial pharmacovigilance, where you are essentially dividing the number of incidents by the person-time or the number of patients in the cohort overall, in passive PhV, only incidents are reported. This makes it quite difficult to figure out their prevalence overall, but fortunately, we have some metrics we can use to better understand the issues with a particular medication or vaccine. The proportional reporting ratio (PRR) is a metric that can operate entirely on spontaneous reporting, and reflect how frequent a particular symptom is for a particular treatment versus all other treatments.

Defining PRR

For convenience’s sake, I will use the subscript * operator to mean a row or column sum of a matrix, so that

N_{i,*} = \displaystyle \sum_{j=1}^{n} N_{i,j}


N_{*,j} = \displaystyle \sum_{i=1}^{m} N_{i,j}

and furthermore, I will use the exclusion operator * \neg to mean all entities except the right hand value. So e.g.

N_{i, * \neg k} = \displaystyle \sum_{j=1, j \neq k}^m N_{i,j}

Conventionally, the PRR is often defined to with reference to a 2×2 contingency table that cross-tabulates treatments (m axis) with adverse effects (n axis):

Adverse effect of interest
All other adverse effects
(\neg i)
Treatment of interest
a = D_{i,j} b = D_{i, * \neg j} a + b = D_{i, *} = \displaystyle \sum_{j = 1}^{n} D_{i, j}
All other treatments
(\neg j)
c = D_{* \neg i, j} d = D_{* \neg i, * \neg j} c + d = D_{* \neg i, *} = \displaystyle \sum_{k=1, k \neq i}^{m} \sum_{l = 1}^{n} D_{k, l}


With reference to the contingency table, the PRR is usually defined as

\frac{a / (a+b)}{c / (c+d)} = \frac{a}{a + b} \cdot \frac{c + d}{c}

However, let’s formally define it over any matrix D.

Definition 1. PRR. Let D be an m \times n matrix that represents the frequency with which each of the m adverse effects occur for each of the n drugs, so that D_{i,j} (i \in m, j \in n) represents the number of times the adverse effect j has occurred with the treatment i.

For convenience’s sake, let D_{*,j} denote \sum_{i=1}^{m} D_{i,j}, let D_{i,*} denote \sum_{j=1}^{n} D_{i,j}, and let D_{*,*} denote \sum_{i=1}^{m} \sum_{j=1}^{n} D_{i,j}. Furthermore, let D_{* \neg i, j} denote \sum_{k \neq i}^{m} D_{k,j} and D_{i, * \neg j} denote \sum_{k \neq j}^{n} D_{i, k}.

Then, PRR can be calculated for each combination D_{i,j} by the following formula:

PRR_{i,j} = \frac{D_{i,j} / D_{i,*}}{D_{* \neg i, j} / D_{* \neg i, *}} = \frac{D_{i,j}}{D_{i,*}} \cdot \frac{D_{*\neg i, *}}{D_{*\neg i, j}}

Expanding this, we get

PRR_{i,j} = \frac{D_{i,j}}{\displaystyle\sum_{q=1}^n D_{i,q}} \cdot \frac{\displaystyle\sum_{r=1, r\ne i}^{m} \displaystyle\sum_{s=1}^{n} D_{r,s}}{\displaystyle\sum_{t=1, t\ne i}^{m} D_{t,j}}

Which looks and sounds awfully convoluted until we start to think of it as a relatively simple query operation: calculate the sum of each row, then calculate the quotient of the ADR of interest associated with the treatment of interest divided by all uses of the treatment of interest on one hand and the ADR of interest associated with all other drugs (j \mid \neg i or c) divided by all ADRs associated with all treatments other than the treatment of interest. Easy peasy!

Beyond PRR

However, the PRR only tells part of the story. It does show whether a particular symptom is disproportionately often reported – but does it show whether that particular symptom is frequent at all? Evans (1998) suggested using a combination of an N-minimum, a PRR value and a chi-square value to identify a signal.[1] In order to represent the overall safety profile of a drug, it’s important to show not only the PRR but also the overall incidence of each risk. The design of the SafeGram is to show exactly that, for every known occurred side effect. To show a better estimate, instead of plotting indiviual points (there are several hundreds, or even thousands, of different side effects), the kernel density is plotted.

This SafeGram shows four vaccines – meningococcal, oral and injectable polio and smallpox -, and their safety record based on VAERS data between 2006 and 2016.

The reason why SafeGrams are so intuitive is because they convey two important facts at once. First, the PRR cut-off (set to 3.00 in this case) conclusively excludes statistically insignificant increases of risk.[2] Of course, anything above that is not necessarily dangerous or proof of a safety signal. Rather, it allows the clinician to reason about the side effect profile of the particular medication.

  • The meningococcal vaccine (left upper corner) had several side effects that occurred frequently (hence the tall, ‘flame-like’ appearance). However, these were largely side effects that were shared among other vaccines (hence the low PRR). This is the epitome of a safe vaccine, with few surprises likely.
  • The injectable polio vaccine (IPV) has a similar profile, although the wide disseminated ‘margin’ (blue) indicates that ht has a wider range of side effects compared to the meningococcal vaccine, even though virtually all of these were side effects shared among other vaccines to the same extent.
  • The oral polio vaccine (OPV, left bottom corner) shows a flattened pattern typical for vaccines that have a number of ‘peculiar’ side effects. While the disproportionately frequently reported instances are relatively infrequent, the ‘tail-like’ appearance of the OPV SafeGram is a cause for concern. The difference between meningococcal and IPV on one hand and OPV on the other is explained largely by the fact that OPV was a ‘live’ vaccine, and in small susceptible groups (hence the low numbers), they could provoke adverse effects.
  • The smallpox vaccine, another live vaccine, was known to have a range of adverse effects, with a significant part of the population (about 20%) having at least one contraindication. The large area covered indicates that there is a rather astonishing diversity of side effects, and many of these – about half of the orange kernel – lies above the significance boundary of 3.00. The large area covered by the kernel density estimate and the reach into the right upper corner indicates a very probable safety signal worth examining.


A SafeGram for each vaccine shows the two-dimensional density distribution of two things – the frequency and the proportional reporting rate of each vaccine (or drug or device or whatever it is applied to). When considering the safety of a particular product, the most important question is whether a particular adverse effect is serious – a product with a low chance of an irreversible severe side effect is riskier than one with a high probability of a relatively harmless side effect, such as localized soreness after injection. But the relative severity of a side effect is hard to quantify, and a better proxy for that is to assume that in general, most severe side effects will be unique to a particular vaccine. So for instance while injection site reactions and mild pyrexia following inoculation are common to all vaccines and hence the relative reporting rates are relatively low, reflecting roughly the number of inoculations administered, serious adverse effects tend to be more particular to the vaccine (e.g. the association of influenza vaccines with Guillain-Barré syndrome in certain years means that GBS has an elevated PRR, despite the low number of occurrences, for the flu vaccines). Discarding vaccines with a very low number of administered cases, the SafeGram remains robust to differences between the number of vaccines administered. Fig. 1 above shows a number of typical patterns. In general, anything to the left of the vertical significance line can be safely ignored, as they are generally effects shared between most other vaccines in general and exhibit no specific risk signal for the particular vaccine. On the other hand, occurrences to the right of the vertical significance line may – but don’t necessarily do – indicate a safety signal. Of particular concern are right upper quadrant signals – these are frequent and at the same time peculiar to a particular vaccine, suggesting that it is not part of the typical post-inoculation syndrome (fever, fatigue, malaise) arising from immune activation but rather a specific issue created by the antigen or the adjuvant. In rare cases, there is a lower right corner ‘stripe’, such as for the OPV, where a wide range of unique but relatively infrequent effects are produced. These, too, might indicate the need for closer scrutiny. It is crucial to note that merely having a density of signals in the statistically significant range does not automatically mean that there is a PhV concern, but rather that such a concern cannot be excluded. Setting the PRR significance limit is somewhat arbitrary, but Evans et al. (2001) have found a PRR of 2, more than 3 cases over a two year period and a chi-square statistic of 4 or above to be suggestive of a safety signal. Following this lead, the original SafeGram code looks at a PRR of 3.0 and above, and disregards cases with an overall frequency of 3Y, where Y denotes the number of years considered.


The SafeGram inherently tries to make the best out of imperfect data. Acknowledging that passive reporting data is subject to imperfections, some caveats need to be kept in mind.

  • The algorithm assigns equal weight to every ‘symptom’ reported. VAERS uses an unfiltered version of MedDRA, a coding system for regulatory activities, and this includes a shocking array of codes that do not suggest any pathology. For instance, the VAERS implementation of MedDRA contains 530 codes for normal non-pathological states (e.g. “abdomen scan normal”), and almost 18,000 (!) events involve at least one of these ‘everything is fine!’ markers. This may be clinically useful because they may assist in differential diagnosis and excluding other causes of symptoms, but since they’re not treated separately from actually pathological symptoms, they corrupt the data to a minor but not insignificant extent. The only solution is manual filtering, and with tens of thousands of MedDRA codes, one would not necessarily be inclined to do so. The consequence is that some symptoms aren’t symptoms at all – they’re the exact opposite. This is not a problem for the PRR because it compares a symptom among those taking a particular medication against the same symptom among those who are not.
  • A lot of VAERS reports are, of course, low quality reports, and there is no way for the SafeGram to differentiate. This is a persistent problem with all passive reporting systems.
  • The SafeGram gives an overall picture of a particular drug’s or vaccine’s safety. It does not differentiate between the relative severity of a particular symptom.
  • As usual, correlation does not equal causation. As such, none of this proves the actual risk or danger of a vaccine, but rather the correlation or, in other words, potential safety signals that are worth examining.
Grouped by pathogen, the safety of a range of vaccines was examined by estimating the density of adverse event occurrence versus adverse event PRR. Note that adverse events reported in VAERS do not show or prove causation, only correlation. This shows that for the overwhelming majority of vaccines, most AEFI reports are below the PRR required to be considered a true safety signal.

SafeGrams are a great way to show the safety of vaccines, and to identify which vaccines have frequently occurring and significantly distinct (high-PRR) AEFIs that may be potential signals. It is important to note that for most common vaccines, including controversial ones like HPV, the centre of the density kernel estimate are below the margin of the PRR signal limit. The SafeGram is a useful and visually appealing proof of the safety of vaccines that can get actionable intelligence out of VAERS passive reporting evidence that is often disregarded as useless.

References   [ + ]

1. Evans, S. J. W. et al. (1998). Proportional reporting ratios: the uses of epidemiological methods for signal generation. Pharmacoepidemiol Drug Saf, 7(Suppl 2), 102.
2. According to Evans et al., the correct figure for PRR exclusion is 2.00, but they also use N-restriction and a minimum chi-square of 4.0.

Out for tapas with Katie and Dad!

Pata Negra is an excellent little tapas place near the riverside, halfway between the hill we live on and Újlak to the north. The food is sometimes a little hit and miss – the red wine chorizo is great, but some staples are not that brilliant and others are outright odd. Still, overall a great place with decent atmosphere and a Sangría that should come with its own weekend safety brief  ⭐️⭐️⭐️⭐️

Taken on Feb 25, 2018 @ 20:16 near Pata Negra Budapest, this photo was originally posted on my Instagram. You can see the original on Instagram by clicking here.

Krak’n Town is crackin’!

Krak’n Town is crackin’! We visited Budapest’s one and only steampunk themed restaurant for a belated Valentine’s Day dinner, and had an absolute blast. Great place, good atmosphere and quirky yet yummy dishes! Highly recommended. ⭐️⭐️⭐️⭐️⭐️

Taken on Feb 15, 2018 @ 17:45 near Krak'n Town, this photo was originally posted on my Instagram. You can see the original on Instagram by clicking here..

Ebola! Graph databases! Contact tracing! Bad puns!

Thanks to the awesome folks at Neo4j Budapest and GraphAware, I will be talking tonight about Ebola, contact tracing, how graph databases help us understand epidemics and maybe prevent them someday. Now, if flying to Budapest on short notice might not work for you, you can listen to a livestream of the whole event here! It starts today, 13 February, at 1830 CET, 1730 GMT or 1230 Eastern Time, and I sincerely hope you will listen to it, live or later from the recording, also accessible here.

An epitaph on a life of service

They say your first boss is your most memorable one – the one that shows you the ropes about what work means and how to do it. This is not about my first boss, but my most memorable one. She wasn’t even my boss for particularly long, but only for the few months of a summer internship at the European Parliament. But she passed on some lessons to me that I might not always have been able to live up to, but I sure as anything never forgot.

It was the summer after my first year at Oxford, and my time in Brussels seemed to start under an ill omen: the turbine cowling of the plane I flew in on detached during landing, leaving the travelers on the starboard side seated around the wing screaming like a class of schoolkids on a rollercoaster. For that reason, we had to land at a divert field, which was out in the middle of nowhere, and my escort, whose phone number I did not know, was waiting for me at the other airport. My entry passes weren’t ready. And, of course, not only was I late for my first day because I inherited my father’s inability to read a map, I also had a whole flock of butterflies in my stomach.

“You’ve… grown!”, I heard her say immediately as she saw me. I hastily tried to recall when we last met – it was, I eventually recollected, more than half decade earlier, at a state dinner during her tenure as ambassador to Vienna, to which my father let me tag along, that we last saw each other. Her husband, a keen yachtsman, quite enjoyed having someone to ‘talk shop’ with, something he certainly did not seem to have had much occasion to in Vienna. And there I was, so many years later, in an almost entirely different world – she was now an MEP,[1] I finished my first year in Oxford a few weeks earlier. I have gone from a chubby four-foot-something to a muscular 6’2″, no doubt helped by my physically and mentally intense freshman year. And with that single sentence, she dispelled all my anxiety and apprehension.

In retrospect, it’s silly how something so irrelevant could put me at ease immediately. I would learn, eventually, that this was part of her superpower. She was not a career politician. She was not a career diplomat, though she could be plenty diplomatic. She was far from a career Eurocrat. But she had the skill to put everyone at ease, find a voice with a range of people and say the right thing every time. In my personal diary, I wrote this about her style: “she could talk to butterflies.[2] And that included not merely her ability to talk to everyone of all ranks and stripes, but a character that earned a begrudging respect even from her fiercest rivals.

She was not a believer in equal opportunities, but in fairness to all and responsibility according to merit. With my area of responsibility focusing on the Single European Sky Air Traffic Management Research and the Galileo GPS network, not only did she not mind taking advice and asking questions from a barely twentysomething intern, she relished it. The same went for everyone else – she took pleasure in learning new things and she enjoyed how such occasions confirmed that she picked right people for her staff. I would run meetings with experts, talk to stakeholders, write draft legislation and be the last to leave the office. And we had a blast.

On the last day on the job, she took me for a stroll across Parc Léopold, sheltering in the shadow of the European Parliament’s Hémicycle and the Solvay library.[3] Others, I suppose, did appraisals – she bought us some French fries from a nearby stall, sat me down on a bench and taught me one of the greatest lessons of my life. I remember every moment like it is seared into my mind, and I hope never to forget her words.

“Service,” she would say, “is not about doing a job for a paycheck. It’s not about doing a job for the money. It’s not doing a job for the perks. Many will wonder why you chose to serve rather than being served. Some will make you feel unappreciated. But if I thought you’re after the easy path or if I thought you couldn’t handle watching others have an easier time, we wouldn’t be having this conversation.”

“You see,” she said, tossing a few French fries to the hungry ducks, “service is about doing what is right, because it’s the right thing and because you’re the right person to do it, and damn the consequences. And more often than not, it will be hard, unpleasant and sometimes even painful. You need to remember why you’re doing what it is you’re doing.”

“Now, I don’t know what you’ll end up doing,” she continued, almost as if she had somehow sensed my incipient misgivings about a career in public office. “But I know that you want to serve. I know that you want to do well, at all costs. I know that you want to see the job through. I know you want to do it with courage and honour, whomever or whatever you serve – your family, your nation, your people, or even humanity. And I know you chose that life out of your own volition, knowing it won’t be easy. But I also know there’s nothing on God’s green Earth that could make you happy other than service.”

“So find where you’re needed, run towards the fire, and don’t ever forget why you’re doing what you do.”

“Don’t you ever forget.”

It’s been many long years since that talk, and much has changed. I’ve climbed mountains and dug my way out of holes to find my way to that service that will sustain me. Her words have echoed with every reveille and with every moment on the verge of falling asleep on the keyboard, with every mile run and with every triumph and every failure. And if I am ever blessed to have children, I hope I will have the chance to pass this simple yet deep wisdom on to them.

As I write this, a cold, chilly, clear February winter night’s winds howl outside. I can hear the soft breathing of my gorgeous wife next to me, and the tiny snores of our kitten at the foot of the bed, occasionally stirring. And tomorrow is another day, another challenges and another set of service.

Dr. Barsi Pataky Etelka ran the course, and ran it with courage, strength and a commitment to service I have not often witnessed. Born in 1941, she trained as an architect and engineer. In 1990, with the fall of the communist terror regime, she would enter the political arena, eventually spending a tenure in Parliament and serving as Hungary’s ambassador to Vienna. In 2003, she was among the first batch of MEPs elected from Hungary, and became responsible for Europe’s ATC research and the development of Galileo, the EU’s global geospatial positioning system. Since 2009, she has been President of the Hungarian Chamber of Engineering and since 2010, a Governmental Commissioner for the Danube Regional Strategy. Dr. Barsi Pataky passed away yesterday, at the age of 77.

She has been married to the love of her life, the engineer, merchant and life-long legendary yachtsman István Barsi, for 44 years, until his death in 2012. Theirs was a kind of love that young men aspire to for their older days; a love that carried both of them through stormy waters.

To those she allowed in her confidence and mentored, however briefly, she will never be gone. She will be there, in our consciences and our thoughts, encouraging us to find where we are supposed to be of service and do so. And as long as we try to do our duty, as the Lord and our skills and talents give us the light to see it, she will live on.

References   [ + ]

1. Member of the European Parliament
2. That’s not to be taken literally. It is from a Kipling poem called True Royalty:

There was never a Queen like Balkis,
From here to the wide world’s end;
But Balkis talked to a butterfly
As you would talk to a friend.

There was never a King like Solomon,
Not since the world began;
But Solomon talked to a butterfly
As a man would talk to a man.

She was Queen of Sabaea—
And he was Asia’s Lord
But they both of ’em talked to butterflies
When they took their walks abroad.

3. Famous for being the scene of the Solvay Conferences, including the Fifth Solvay Conference, commemorated in the immortal photo that has basically all luminaries of interbellum physics.

In extremis

It’s not frequent for a State of the Union address to delve into drug approval policy in any depth. Yet that’s exactly what President Trump did when, for the first time, he spoke publicly about legislation allowing terminally ill patients to access experimental treatments that have passed only FDA Phase I trials, often referred to as ‘right to try’ legislation:

We also believe that patients with terminal conditions should have access to experimental treatments that could potentially save their lives. People who are terminally ill should not have to go from country to country to seek a cure — I want to give them a chance right here at home. It is time for the Congress to give these wonderful Americans the ‘right to try’.

The Right to Try is unsurprisingly controversial. On one hand, patient groups see it as a chance to access treatments that are too far in the pipeline for them. It is hard not to have sympathy with this argument. It is especially hard for me to do so so, because my life was saved by an experimental drug that at the time did not have general approval for my condition, though it was known to be safe. At the same time, FDA Commissioner Scott Gottlieb is right to be skeptical about this policy effectively usurping the FDA’s authority to ensure that pharmaceuticals administered to all patients in the United States are safe and effective. Like all great moral quandaries, both sides are, to an extent, right.

What is ‘right to try’?

Quite simply put, right to try laws allow terminally ill patients access to treatments, medications and devices that have passed FDA Phase I testing, but are not yet approved by the FDA. The libertarian Goldwater Institute, which has been pushing and lobbying for right to try, has created a model legislation, variants of which have by now been accepted by 38 states. It provides, in short, an exception for patients suffering from “advanced illness”, defined as

a progressive disease or medical or surgical condition that entails significant functional impairment, that is not considered by a treating physician to be reversible even with administration of current federal drug administration approved and available treatments, and that, without life-sustaining procedures, will soon result in death.[1]

Patients that qualify under this definition would then be allowed access to any treatment, pharmaceutical or device as long as it has passed Phase I testing,[2] although the manufacturer or provider would be under no obligation to sell or provide that treatment to the patient.

Ethical issues

The ‘right to try’ legislation is far from uncontroversial. @gorskon, whom I greatly respect even when I disagree with him, has gone so far as to call it a ‘cruel sham’ and a libertarian attack on the FDA, and his points merit consideration:

I’ve written many times before over the last three years about how “right-to-try” laws have swept the states. When last I wrote about right-to-try, 37 states had passed such laws over the course of a mere three years, and I observed at the time that it wouldn’t surprise me in the least if most or all of the remaining states were to pass such laws within the next year or two. Basically, the idea behind these laws is that the FDA is killing patients (I’m only exaggerating slightly) through its slow drug approval, overcaution, and bureaucratic inertia, or at least letting them die because life-saving drugs are being held up. So the idea, hatched by the Goldwater Institute was that terminally ill patients should have the “right-to-try” experimental drugs not yet approved by the FDA because they have nothing more to lose. Of course, it’s not true that they have nothing more to lose, but I’ll discuss that more later. Basically, right-to-try laws purport to allow the terminally ill “one last shot” by letting them access experimental therapeutics outside of FDA-sanctioned clinical trials. However, these laws operate under a number of false assumptions, not the least of which is the caricature of the FDA as being slow, inefficient, and unwilling to bend, as you will see. They also strip away a number of protections for patients, as you will also see.

While I am not sure I’m on board with the idea of there being a libertarian conspiracy to curb the FDA’s powers – especially given how limited the ambit of right to try legislations would be -, Orac makes an excellent point.

Much of the Goldwater Institute’s position is premised on the FDA being ‘slow’ and inefficient – as they like to present their case, they merely seek to remedy an instance of the state failing to serve citizens adequately. Speaking from personal experience, when you’re dying, everything is too slow and no approval process can come fast enough. It is hard not to have a lot of sympathy towards the patients who know there may be a promising drug in the pipeline but like Moses of old, they will never get to see the promised land. But realistically, the FDA is not slow – indeed, it is as fast as, or sometimes even faster, than regulatory agencies in many other countries.[3]

I would also add that the benefits of investigational therapies has rarely been particularly high, with only about 10% yielding a clinical improvement.[4]. For 90% of patients, then, the right to try would mean putting themselves through another round of torturous treatment instead of spending their last weeks or months focusing on appropriate symptom relief, quality of life and putting their affairs in order. In the end, these might be more important than a forlorn hope of extending one’s life by another few months.

Patients are subject to a high degree of informational asymmetry. When I had to decide between various treatments, I spent days on PubMed, reading every single study, building my own little mini-metaanalysis from my hospital bed. I was lucky – I had access to all the academic literature I could want and I was trained in evaluating that evidence. But most patients aren’t (and there’s no reason why they would be!),[5] and what takes the place of sound knowledge is often less healthy. Patients may feel emotional pressure to try every treatment, however modest the chance of success: be it because they would feel that not doing so is ungrateful towards the doctors who ‘fought for them’, or because they feel they owe it to their family, the psychological pressure to try potentially ineffective treatments is immense, and might rob the patient from their chance to exercise some degree of autonomy over the last moments of their life.

The reverse of the medal

At the same time, many note, respect for the patient’s autonomy should extend to allowing treatment that a competent patient wants, even if the physician disagrees. And, in addition, many argue that it would be paradoxical to allow patients to outright request physician-assisted suicide but not the administration of a treatment that may just save their lives. These arguments are not pointless, and any policy needs to justify why paternalism is particularly justified in this case, and while treatment would be inappropriate where suicide would be permitted.

More importantly, it is arguable that the absence of a ‘right to try’ leads to its own set of tragic adverse consequences, by directing patients to ‘try’ treatments in the unregulated sector of outright quackery. I had the distinct misfortune of witnessing one of these.

Jillian Mai Thi Epperly is an unqualified naturopathic healer with no educational background in nutrition who is running what she describes as a large-scale experiment on volunteers (aka marks). Her victims – around 30,000 – joined her Facebook group, which is closer to a cult than anything else, and consume vast quantities of a concoction that contains an unhealthy amount of salt and fermented cabbage juice. This is supposed to rid the body of ‘weaponised mutant candida and parasites’, which she claims is responsible for all or most pathological processes in the human body. Ms Epperly’s Facebook group is replete with images generally for the strong of stomach (including gut lining which her acolytes believe are parasites), but that’s nothing compared to the damage she has done to human lives. None is more tragic than the story of J. (name redacted in the interests of privacy), who is suffering from an unspecified cancer, and who was one of the biggest supporters of the ‘protocol’… until the placebo effect wore off, and she realised it is all a fraud. But valuable time spent on a miserable, painful treatment that bore no benefit, and might well accelerated J.’s disease progression.

There are, as we speak, thousands, if not millions, of Jillian Epperlys, peddling their fraudulent wares to an uninformed public. When the chips are down and conventional treatment options have been exhausted, patients will always turn to alternatives. With Right to Try, they could do so under medical supervision, adequately counseled and with their side effects managed. Moreover, the medications administered would have to adhere to standards of manufacture (GMP) and have a well-understood mechanism of action in most cases. There will always be desperate patients – and a well-designed Right to Try policy may keep them away from quacks and within the traditional medical system that would cater better for their needs and handle the transition from trying salvage/last-ditch treatments to palliative care and ensuring adequate end-of-life care.

Another undesirable aspect is the existence of an informal right to try. Darrow et al. describe the case of Josh Hardy, a 7-year-old boy who received the experimental antiviral drug brincidofovir after the media drew sufficient attention to his case for the manufacturer to ‘add’ Josh to an open-label study.[6] Similarly, public sympathy for the aid workers from Samaritan’s Purse, including Kent Brantly, allowed for the use of the chimeric monoclonal antibody ZMapp. From the perspective of health equity, it is concerning that this informal procedure is amenable only to those with the means and connections to launch a massive social media campaign. In this sense, it is eerily reminiscent of the case of Sarah Murnaghan, whose lung transplant ineligibility was supervened by a large public campaign. It is fair to question whether the effects of a discretionary scheme that ultimately favours those with social, political and economic influence would not be better supplanted by a formal, equitable system available to all on equal terms.

The light and the dark

I don’t normally discuss end-of-life policy or bioethics: my days in that field are long gone, and my priority now is to try to avert those situations. However, to me, Right to Try will always be more than an abstract issue. A few years ago, a last-ditch therapy ended up working so well, it saved my life and put me into remission. After failing two different treatment regimens, we were out of conventional options, and things looked bleak – until a dedicated consultant oncologist took on the drug manufacturer, the hospital board and even the government, so as to be allowed to administer a drug still not approved for the particular indication. It was a huge gamble, and it worked. I will forever be grateful for the chance I’ve been given – but I’m also aware that I was the exception, not the rule, and n=1 doth not a good rule make.

I believe that even if the current version of Right to Try is, as Orac says, a ‘cruel sham’, it does not inherently have to be so.

There is enormous potential in Right to Try policies, not only for patients but also for drug development and future patients. Well implemented, it does not have to be a cruel sham. Nor does it necessarily have to be a wholesale ouster of the FDA’s competence.

But if it is to be anything other than that, it has to come with a comprehensive institutional structure that ensures that consent is truly free and adequate. Crucially, an independent physician must be available to honestly explain the odds and assess the patient’s understanding and capacity.[7] The process must focus on balancing respect for patient autonomy against a degree of paternalism needed to protect a vulnerable patient. And in the end, it is paramount to have a sensitive understanding of the potential pressures the patient is under. It is not an easy task. But it is not an impossible one.

Many states now speak of ‘death with dignity’ as a euphemism for physician-assisted suicide. Perhaps to some people, that indeed is dignity, and it is a choice that deserves consideration. It is not cowardice or refusal to fight. But what about patients whose concept of dignity would closer encompass ‘staying in the fight’? Whether it is right or wrong, the practice of physician assisted suicide has shown that true consent can be separated from impaired consent in such a difficult scenario. Why, then, would it be impossible to separate instances where the Right to Try would merely engender false hope from those where it might have a small but not unrealistic clinical chance to succeed?

In the end, one needs to be able to separate the present rules from the principle. The present rules, and much of the motivation behind it, are clearly imperfect. But the potential behind Right to Try is significant. Regulated Right to Try can curb quackery and unregulated charlatans preying on the incurably ill by providing more legitimate last-ditch treatments carried out under medical supervision. It can accelerate research without prejudicing patient welfare if the pharmaceutical manufacturer is kept at arm’s length. And maybe, just maybe, it can save lives.

The current legislative framework might not be there yet. But it has the potential to make a difference not just to research but for millions of patients who have exhausted all possibilities, who, like me, might strike gold. Just as the history of science is one of incremental development, procedures and practices should be given the chance to develop over time.

References   [ + ]

1. Right to Try Model Legislation, sec.1(2)(a).
2. Ibid., sec.2(1).
3. Downing, N.S. et al. Regulatory review of novel therapeutics – comparison of three regulatory agencies. N Engl J Med 366:2284-2293.
4. Freireich, E.J. et al. The role of investigational therapy in management of patients with advanced metastatic malignancy. J Clin Oncol 27:304-306.
5. Woloshin S, Schwartz LM, Welch HG. Patients and medical statistics: interest, confidence, and ability. J Gen Intern Med 20:996-1000.
6. Darrow, J.J. et al. Practical, Legal and Ethical Issues in Expanded Access to Investigational Drugs. N Engl J Med 372:279-286.
7. In all honesty, I am not entirely sure that all too many patients in that emotionally and physically difficult situation are lucid enough to comprehend the entirety of what is involved in such a decision!

Five years

Five years ago, the love of my life boarded a plane in DC and landed in London. She didn’t know what she was getting into, and I guess there were times that were beyond what she bargained for. Later that year, we got civilly married. She stood by me as I was recovering from a life threatening illness, she helped me find normalcy, and gave me the five best years of my life. Happy sort of anniversary, Katie. I love you to MACS0647-JD and back.

Taken on Jan 20, 2018 @ 00:00 near Budapest, Hungary, this photo was originally posted on my Instagram. You can see the original on Instagram by clicking here.

The cult of suffering

In a recent tweet, @NewWorldHominin – also known as Lindsay Shepherd and famous for her very public conflict with her employer, Wilfrid Laurier University of Waterloo, Ontario, over showing a video of Jordan Peterson – posted a curious excerpt from Angela Nagle’s book Kill All Normies (what a title!), a short history of the most recent skirmishes in the online culture wars.[1] Nagle writes:

[Progressive political scientist, activist and UPenn professor] Adolph Reed Jr. has often said liberals don’t believe in actual politics any more [sic], just ‘bearing witness to suffering’. The cult of suffering, weakness and vulnerability has become central to contemporary liberal identity politics, as it is enacted in spaces like Tumblr. It is also common … to openly identify themselves as having disabilities and mental health issues that make them, by their own admission, extremely vulnerable and suffering.

I am largely unconcerned with the political aspects of his statement. I am not a political scientist, and the politics of this issue are of no interest or concern to me.[2] At the same time, society’s relation to pain, and the historical development of vulnerability and suffering, has been a pervasive interest of mine for most of my life. It is not entirely a matter of detached academic interest, either. I don’t normally talk about my own experience with pain: not only do I believe we all experience pain very differently and the neurophysiological processes involving afferent C fibres and all that jazz are only part of what we cognitively conceive of pain, but I’m also the product of a ‘boys don’t cry’ upbringing that shunned even really talking about all that. I have removed 3″ metal splinters from my upper arm and stitched up the resulting wound and went about my way, because, well, it was so normal. I have spent most of my life in severe – some would say excruciating – pain. Unlike the relatively simple pain of a nasty headache or a paper cut, chronic pain is not merely pain that takes longer to resolve, but an entirely different animal. And I have also devoted much of my life to alleviating pain and suffering, in various ways. It’s my subtle revenge on the imperfections of my physiology. Suffering, of course, is a somewhat different animal from pain, but not unrelated. And so, when reading Nagle discuss this ‘cult of suffering’, I was thinking about it partly as an individual witness to the phenomenon of pain – but also a witness to what a ‘cult of suffering’ indeed means to us as a society.

It is important, at this point, to delineate certain terms. When I refer to a ‘cult’ in this context, I am not referring to the modern meaning of the word – as a fundamentalist, often secretive and usually destructive religious movement. Nor am I referring to particular religious practices pertaining to a single deity or demigod, such as the Cult of Dionysius, the Eleusian Mysteries, the cult of Zeus Lykaios in Arcadia or the drug-fueled orgies of the Orphic Mysteries. Actually, most of these mystery religions eventually devolved into drug-fueled orgies that would have made 1970s Los Angeles blush, but that’s not what made them cults – they were ‘cults’ in the sense that they involved secret, set-apart mysteries reserved to the initiated and were in worship of a particular deity. This is closer to what we’re dealing with here, but it is not the relevant interpretation here, either.

Rather, I’m using the concept of a ‘cult’ to describe a set of social practices and methodologies intended to process some overwhelming human experience and integrate it into the way humans understood the world. The Orphic narrative, for instance, which retells the story of the poet Orpheus descending into the Netherworld to bring back Persephone to the land of the living, was an attempt to conceptualise and explain the changing seasons. The same death-rebirth aspect befell Bacchus, God of Wine, because grapes don’t grow all year, either. The ‘cultic’ part I’m concerned with is not about worshipping Bacchus or Persephone/Orpheus, but the fact that a set of notions – conventions, practices, songs, plays, narratives, actions, prayers, etc. – existed through which something cognitively-intellectually inconceivable was enacted communally, and thus, in a sense understood communally.

In that sense, a cult of suffering is not an inherently negative phenomenon. In fact, it is an acknowledgement that when someone is suffering, everybody can – and should – share in that suffering so that everybody could – and should – share in the healing. And there are, in fact, serious moral costs to not sharing this suffering as a community, to leaving the sufferer alone. No single work of human creation has tapped into the hidden heart of the human mystery of pain as profoundly as Sophocles’ Philoctetes, which in a sense deals exactly with what happens when the cult of suffering is absent. It is through understanding the cost of leaving the sufferer alone that we understand the importance and meaning and contribution of a cult of suffering to communal human existence.

Wails from Lemnos (aka ‘oh God, not more Greek drama, please!’)

The Trojan War has been raging on for the best part of a decade. The siege has whittled away the best warriors of both sides. Patroclus is dead, and so is his friend Achilles. Hector is dead. Ajax has taken his life in shame. Everyone is weary of the war, and there seems to be no end in sight, just the tiresome, mindnumbing bloodshed of daily combat. Until one day, the seer Helenus, son of King Priam of Troy, was captured and forced to tell the Greek commanders that they will not be able to prevail against Troy unless and until they have the bow of Heracles.

The bow of Heracles was a legendary weapon, equipped with arrows dunked in the poison of the Hydra. They were awarded to the Greek warrior Philoctetes by a dying Heracles himself, for ending his suffering by lighting his funeral pyre.[3] Years later, Philoctetes was part of the Greek host sailing to Troy to reclaim Helen. On the voyage to Troy, however, Philoctetes’s foot was bitten by a snake, causing a wound that continued to torment and fester but would not heal. For days, the Greeks were distressed by the stench of the wound, kept awake by the wails of Philoctetes and more than a little discomforted by the belief that such injuries were a sign of moral pollution – miasma – that would follow the Greek army and bring misfortune upon them. So, on the advice of Odysseus, the king of Ithaca and the Greek forces’ chief intelligence officer, one night they stranded Philoctetes on the unpopulated island of Lemnos – alone, with only his bow, and his suffering, his pain, his festering wound – and sailed on to Troy.

One can barely imagine Philoctetes’ anguish. For not only is he suffering physically, but also morally, wounded by the Greeks’ betrayal:[4]

Imagine my surprise when I awoke, the tears I shed, the sound of my sadness.

All of the ships in the fleet had vanished.
Alone with my infection, I knew only pain.
Time demanded that I scavenge for food with this sacred bow, which saved my life.

I would crawl through deep mud on stiff knees, scraping my rotten foot against rocks.
When water was scarce, I survived by collecting ice.
I spent cold winter nights without fire, but rubbing stones together for their spark, I saved myself from certain death.

The true tragedy of Philoctetes was not just his snakebite: it was his abandonment.[5] And the Greeks’ betrayal, leaving a wounded comrade behind, echoes through the ages. Modern militaries often speak of ‘leaving no man behind’, because if there’s one way to compound pain, it is to do so by making the person suffer alone. It morally degrades the victim, but also the perpetrator.

Unlike most tragedies, Philoctetes does have something approaching a happy ending, or at least a resolution. Odysseus and Neoptolemus, the young and recently orphaned son of Achilles, sail to Lemnos to mend ties and restore the relationship between Philoctetes and the Greek army, although in a typical Odyssean underhanded manner. In the end, there is – with the divine intervention of Heracles himself – a reconciliation. That reconciliation is, importantly, communal: Philoctetes cannot heal unless he returns to his community, the Greek army at Troy, and the Greeks cannot ‘heal’ and prevail in battle unless they mend the ties with the suffering warrior they so disgracefully betrayed. The message here is that from certain wounds, we can only heal as a community: only through sharing what we have been through, through communal rituals of processing trauma, through the reintegration of the wounded or sick person into society can healing take place.

When Sophocles wrote Philoctetes, he was in his late 70s. He has served as a general at least twice, in a century of near-constant warfare. His actors were citizen-soldiers, and so was much of his audience – all of it in need of healing from the traumata of war, loss and grief. Theatre, as the Athenians practiced it, was not entertainment – it was social psychotherapy, a form of group psychodrama that allowed them to grieve and heal together. It was a cult of suffering in the best sense possible.

Sharing and processing

The reason why Athenian drama therapy was so extremely successful was that it began with a highly egalitarian premise: we have all suffered, albeit in different ways, and we all deserve to heal. The primary objective was to expose traumatic histories to allow re-integration into society. It is often witnessed, for instance, that once a victim of a traumatic experience can narrate what happened to them, they gain a degree of control over it: they can conceive of themselves no longer as mere victims but as survivors and of the traumatic past not as a secret locked away in a hidden box of shame but something that they now have control over. We are narrative beings, and our principal way of asserting control over our experiences is to shape them into a narrative. That is trauma processing.

It is a fearsome process, and a fairly difficult one. For the longest time after surviving HLH, I have not been able to talk about it at all. I would perhaps mention occasional flashes of the crazy, sad, tragic yet sometimes hilarious experience that going through a nearly always terminal illness was in my early 20s. Self-deprecating humour and silly jokes[6] alternated with moments of intense wistfulness and grief – one defensive mechanism yielding to the next. It wasn’t until I was able to – at the very least internally – tell my story from the beginning to its end, that I felt I could put this experience behind myself. First, I tried to recount it to myself, then to my beloved wife, who did exactly what I needed at the time: to be someone who listens. Processing trauma by verbalising it is scary because – once again, being the narrative creatures we are – it makes things a kind of real. The truly scary part about telling someone what happened to us is not that someone else will hear it – but that we, too, will hear it and have to accept it as real. A long time ago, working pro bono with survivors of political torture, I encountered an extremely polite and well-adjusted young man – almost a little too well-adjusted for what he’s gone through. And while he gave detailed narratives of what was done to him (I’ll spare you the details, but it was all kinds of horrid), he never used the word ‘torture’. Eventually, the staff psychologist picked up on this. Once she got him to reluctantly admit that he was indeed the victim of intense torture – in those words -, he broke down in tears that looked like they would never stop. He has faced the partial reality of his experience, but not the conceptual reality. Now, he had to process and own that part of his experience and his self-understanding. He had to adjust his self-understanding to include not merely the acts he was victim to, but also the notion of being a ‘torture victim’, with all that entailed for his personality.[7]

Facebook dot com slash catharsis

The theatre of Dionysus Eleuthereus, where Sophocles’s celebrated plays were performed, where Athenians first heard the wails of Philoctetes and the mournful agony of Heracles in the Trachinae, could seat over 15,000 people. Around the 5th century BC, that would have amounted to 5% of the whole population of Attica and half to a third of the 30-50,000 or so free male citizens who had the right to vote. Just a stone’s throw from the theatre of Dionysus, on the slopes of the Acropolis, stood the asclepeion of Athens, a combination of a temple, hospital and hospice where the sick came to experience ‘katharsis’: purification through baths, purging, diets and even a predecessor of art therapy. It is no accident that the patients of the Athenian asclepeion were within earshot of the Theatre of Dionysus, where they experienced an entirely different kind of katharsis: the emotional katharsis of the theatre was seen as being as legitimately therapeutic as snakes and purgatives and poultices and salves. The 5th century BC Athenians might have accidentally invented psychodrama.

Now, with the growth of social networks, 15,000 members are hardly a number worth mentioning. People suffering from illnesses or social situations that hardly anyone in their vicinity would be likely to share could immediately find thousands, if not hundreds of thousands, of fellow sufferers. To many, this must be as liberating as Philoctetes escaping his captivity on Lemnos, where he was alone with his grief, sorrow and agony, and find instead literally thousands of fellow sufferers. For example, for a condition as relatively rare as Ehlers-Danlos Syndrome (total prevalence: around 1:5,000-40,000 live births depending on type)[8], there is a major group with over 27,000 members and over a dozen groups with a membership exceeding 5,000 members. Even for relatively rare diseases, such as HLH (prevalence: 1:50,000 live births)[9] groups with several thousand members exist. The purpose of these groups is only partially informative: since most of the members are subjective laypeople (patients or their relatives), better information is available on medical websites and open access journals. Rather, the principal purpose appears to be the creation of a community of sufferers (both those in the first degree, i.e. patients themselves, and those in the second degree, i.e. their caregivers, parents and relatives). Interactions typically focus less on discussing potential treatment options, but rather significantly more on inquiring whether others have experienced a particular side effect or reaction on one hand and validate people who are unsure about their symptoms and diagnoses. And while all this does have an informational aspect, the aspect of a community that subjectively understands is what motivates most people to participate in such discussions.

In many ways, this is an undoubtedly positive development. But while – especially for rare diseases[10] – such communialisation of suffering can alleviate the tormenting isolation reminiscent of Philoctetes’ on Lemnos, there is a dark side to this phenomenon, too.

We’re all mad here

What happens when the communalisation of trauma, misfortune, disease or pain, from Sophoclean plays to Facebook support groups, becomes dysfunctional? It is worth mentioning three possible dysfunctions.

One, the Sophoclean way of communal processing of trauma took place among a heterogeneous population. Certainly, they shared some fundamental experiences, which made for a dramatic language intelligible to all. For instance, the majority of actors and most of the audience watching Ajax’s descent into madness have themselves served and recognized Ajax’s combat trauma – what we in our contemporary language would call PTSD. Certainly many of them knew enough about chronic illness to understand Philoctetes’s anguish. And when they heard the wails of the greatest hero of Greek mythology, the mighty Heracles himself, begging for death in Sophocles’ Trachinae, most could relate it to a similar experience with a dying loved one. But the essence of processing this experience was to do it communally. It was never meant to be an echo chamber. It was not a bunch of citizen-soldiers turned actors putting a play for themselves, but to the Athenian public at large. Unlike the Facebook groups that serve as the modern equivalents of publicly processing grief or anguish, the Ancient Greek drama was meant as a sort of silent dialogue. The audience might not have had anything to say, but they did have something to do. This was for their benefit, too, and their duty was to assist the communal processing of the dramatic experience. Their job was to be the very opposite of the Greek fleet that left Philoctetes suffering alone – their job was to show ‘compassion’, to suffer (‘passion’) with (‘com’) the protagonist. In a homogeneous population, the dynamics are vastly different. Not only is everybody a ‘victim’, those who are not are expressly excluded. There is no hope for reintegration – after all, there’s no interaction with the society to reintegrate with. There is beyond doubt much merit in victims and sufferers living and discovering an experience of community, where they themselves feel no longer alone. But that’s not the experience of katharsis, of healing and of reintegration that communal processing of trauma, between those who are suffering and those who are not, could offer.

Two, the narrative framework that facilitated this communal processing of trauma – that is, the play itself – was abstract for a good reason. The tales of woe that Greek drama shows are not every-day crises. They are irresolvably tragic like the situation of Antigone torn between divine or secular law, they’re almost grotesquely devastating as the fate of Oedipus or they involve, like Medea’s descent into madness, the loss of innocent, valuable lives for no good reason. No-one in Sophocles’ Athenian audience, however blighted by misfortune their lives, would be tempted to compete with the tragic heroes of Ancient Greece. Who would dare compare their fate to that of Ajax, Medea or Oedipus? And who could compete with Philoctetes’ decade-long solitude and agony? So final and devastating were these tragedies that they conveyed, through their absoluteness, the message that trauma is not a competition. The Greeks understood that each individual trauma is a little universe in and of itself, a little infinity, and there is no point in arguing whose corresponding experience was the worst. This allowed Greeks to maintain a sense of perspective: on one hand, quite likely none of them had it as bad as the tragic heroes, but at the same time, deep down, they shared the same struggles and pain and tragedies as the divine Heracles, the mighty Ajax and the great Philoctetes. There was no need for an Olympiad of suffering, because of the almost over-the-top nature of Greek tragic fates that were shocking even given the occasional bloodthirstiness of that civilization.[11] Over-the-top tragedy allowed it to remain abstract, while at the same time elevating it to universality. Where traumatic processing becomes concrete, it loses the ability of its abstraction to provide meaning. It becomes a fragmented tale of individual, competing traumata.

Finally, communal processing of trauma was all about reintegration – it was about closing the door behind the traumatic experience in a sense, and in ‘coming home’ to society. Trauma – and by this, I also include adverse experiences that are not ordinarily thought of as traumatic: a severe illness, a difficult upbringing or a childhood spent on the wrong side of the tracks – alienates us from our host society. Many victims of trauma go so far as to perceive themselves as fundamentally ‘different’ from ordinary human society and experience trouble ‘fitting in’ among those who have not undergone the same experience. The purpose of Greek drama was not to rehash endlessly how broken and different the victims of severe trauma were, but to show them a way back to us, and us a way back to them. In the end, it was about what we had in common rather than about differences. When traumatic processing becomes dysfunctional, it becomes about remaining the ‘other’, the ‘traumatized person’, rather than the person who, with all their traumatic experiences, can no less be integrated into society. Communal processing of trauma does not encourage the development of a highly emphatetic ‘otherness’, a trauma-based self-identity, but advocates a way back to normal society.

On bearing witness to suffering

Reed accuses liberals of ‘just bearing witness to suffering’. In this, I think, there’s a risk of missing the operative word – just. I doubt Reed would object to ‘bearing witness to suffering’. One of the greatest accomplishments of Ancient Greek drama was the validation of the suffering many in those societies have gone through. When citizen-soldiers watched Ajax or Philoctetes, both written by a retired general who knew the cost of teaching and making men inflict violence on others first-hand, they understood they weren’t alone. They understood that unlike the abandoned Philoctetes, they weren’t suffering on a desolate island, but that their pain and anguish were witnessed in some way. And that may have made all the difference.

But just bearing witness to suffering is not enough. For starters, as Reed alleges, it creates this cult of suffering and weakness.

As we have noted earlier, the term ‘cult’ should not necessarily invoke Waco or Jonestown. More subtly, a cult may just be about a shared ritual process, coupled with a shared identity. For instance, those who were inducted into the Eleusinian Mysteries, a mystery religion that evolved from an old farming cult of supplication for good crops, were not only, in a sense, chosen and identified themselves as part of this secret circle of people who could enter the mystery: they also shared a range of ritual practices (much of which involved getting hammered on kykeon, which was basically the ancient Greek version of LSD). Cults develop their own language, their own rules, their own habits, their own moral compass. The cult that Nagle refers to – the cult of ‘suffering, weakness and vulnerability – is no exception.

In a sense, this cult of ‘suffering, weakness and vulnerability’ is a dysfunctional form of communal processing. It is dysfunctional for three reasons:

      • It’s self-enclosed and self-directed. It is not a publicly enacted interactive performance in which there is a dialogue with anyone. It is, at best, an echo chamber. Quite often, the language of ‘owned spaces’ and ‘safe spaces’ is used, to wit, the manifestations of these spaces – virtual or real – should be limited to those ‘initiated into the cult’. There are some legitimate scenarios in which this approach is encountered, e.g. when 12-step groups exclude non-addicts so as to afford addicts a chance to speak openly. But as a social performance, this is failing to build any bridges. Consider the recent trend among Tumblr users to explicitly bar other users from following them unless they, too, are ‘neuroatypical’, ‘disabled’ or some other minority. This creates a curious segregationism that ultimately impedes positive functional outcomes.
      • Processing is always concrete and individual. Elizabeth Martinez coined the term ‘oppression Olympics’ as early as 1993,[12] to describe the controversies that ensue when oppressed minority groups ‘compare’ or ‘rank’ their level of suffering. The genius of Sophoclean tragedy was altogether avoiding this, in two ways. One, the tragedy enacted on stage was so over the top that the audience could not possibly really relate (even in Athens in the 5th century BC, blinding oneself with one’s belt buckle for having accidentally committed incest towards one’s mother was rare enough that Sophocles had not to worry about someone in the audience one-upping poor Oedipus Rex). Two, the overall message of the drama was quite universal. The dramatic heroes fight not against particular forces or power structures that are in some way unique to their station in the world, but against universal human flaws and universal human failings: hubris, fate, ignorance, passion, betrayal. Everybody and nobody at the same time is invited to relate.
      • Processing surpasses the emotional-cathartic and enters the political. The purpose of a Sophoclean drama was to help victims of trauma find their way back to society, and vice versa. It was, primarily, about reconciliation. It was not, at any point, about compensation, about change, about various political rights. The audience may have left with slightly shifted views about some moral issues through the emotional experience of the catharsis, but Sophocles was not Bertolt Brecht.

What Angela Nagle points out as a cult of suffering, weakness and vulnerability rests on two pillars. One of these is the rapid destigmatisation of illness, disability and in particular mental health issues over the last few decades. There is absolutely no doubt to me that this will be recalled as one of humanity’s greatest feats. Partly thanks to a better understanding of the neurobiology of mental illness and partly due to treatments that allow even those with severe mental illness to live productive and socially integrated lives, our outlook on mental vulnerability has changed. At the same time, thanks to various social media platforms such as Facebook, those affected by these issues could experience the ‘safe space’ of an echo chamber.

Love bombing and the cultists of suffering

Ultimately, what Nagle describes as a ‘cult of suffering, weakness and vulnerability’ comes from an inadequate communal way of coping with experiences of suffering, weakness and vulnerability. In most cases, even if the underlying organic or psychiatric disorder is permanent, its effects in terms of suffering, weakness and vulnerability tend to be transient. As time goes on, patients build coping mechanisms that help them function in daily life. But within the dysfunctional ‘support groups’ over the internet, diagnoses are seen as immutable fates that are as part of one’s identity as one’s name or eye colour. The initial experience of being ‘understood’, especially for those suffering from a rare or misunderstood condition, can be overwhelmingly positive – indeed, so positive as to be addictive, and patients will gladly pay the price of not improving as the cost of remaining in this sheltered cocoon where – perhaps, sadly, often for the first time – the efforts it takes to complete every-day tasks with their conditions are appreciated. There is a bigger reward, however.

There exists a pathology known as ‘factitious disorder’ or ‘factitious and/or induced illness’ (FII). In FII, patients are aware they do not have a particular condition, but intentionally induce signs and symptoms to procure treatment. You may have heard it referred to as Munchausen’s Syndrome. It is a very controversial diagnosis, because it is hard to unambiguously separate whether people with FII suffer from a disorder no different from, say, BPD or major depression, or are just exploitative social parasites with a decent streak of sociopathy. People with FII leave a trail of broken people in their wake, theirtrust betrayed and their humanity brutally exploited, and as a consequence of the resulting stigma, we know less about FII than about any psychiatric condition. I recall first hearing about FII in a forensic psychiatry class, and I couldn’t possibly imagine why anyone would even do this. By then, I have been through a few bouts with serious illness, and to intentionally make oneself sick just made no darn sense to me. So after class, I grabbed my professor and asked him why people intentionally assume the sick role, often actually harming their own health.

“That’s the mystery,” he said. “We don’t know. There are so few confirmed cases, and even fewer are willing to talk about it. Why don’t you go and see what you can find?”

I did. I found virtually nothing, save for a small number of females who have been in treatment for FII for some years and offered a valuable insight into their thought process. One point I remember to this day was that while they initially did seek the attention that came from the sick role, what they really, really craved was the role of the ‘fighter’, the strong and resilient person who faces disease and trauma with courage. They wanted to be called brave. They wanted to be called fighters. And more than anything, they wanted someone to acknowledge their actions, praise them and tell them they could be proud of it.[13]

Many of these people came from broken families, and many in today’s cult of weakness come from a broken society. In this broken society, we haven’t decided how to treat young people: we give out participation trophies, but we are afraid to acknowledge true accomplishments lest the less accomplished feel offended. We tell young people they’re the future and they’re going to run the world someday, but we do not expect them to behave like that – and every leader’s education should start with service. We encourage young people to feel ‘pride’, but do not challenge them to accomplish things in which they could feel real pride. We praise every child, then we’re surprised that their self-esteem is low. It is low because kids aren’t idiots. In fact, they’re emotionally more sensitive due to their incomplete maturation of the frontal cortex. They know it’s all bullshit. They know that participation trophies are worthless. They know that they’re fed empty praise by parents and teachers who are scared of them, who are scared of the consequences of emotionally offending any child.[14]

And so, as they see through what Browning called the “forced praise on our part/ the glimmer of twilight“, they hunger for the genuine thing. They hunger for the politically incorrect thing of a first prize medal, for the verboten accomplishment of something at which most people fail, for the absolutely off-limits pride in themselves that can come from a tough job well done. People are willing to risk getting blown up for ridiculously low pay and stupid administrative burdens for a taste of a society that expects, demands and ranks mercilessly,[15] because these things have been expunged from virtually everywhere.

If the sole way young people can find an identity that gives them value and through which they can feel appreciation is by claiming, pretending or role-playing to have various disadvantages, so that they would be measured with the lenient yardstick under which genuine praise betokens even completely mundane, every-day acts (and I can attest as a person with a disability that sometimes getting dressed feels like climbing Everest and going down to the shops, a daunting challenge!), we – and our parents’ generation, who have laid the groundwork for this state of affairs – need to have a conversation. We need to have a conversation on accomplishments, and the need for accomplishments for pride. We need to have a conversation about the fact that everyone is capable of accomplishments worthy of pride and honour. We need to have a conversation about the fact that we have a duty to communally process suffering – not just to witness it and write long-winded 2,200 word heart-wrenchers in Comment is Free but to engage with the existence of suffering, and with those who are going through it, and allow them to reconnect to the society of the ‘healthy’. We need to create a society that has more ambitions for people with disabilities than a socially and economically sidelined existence on benefits.

But more importantly, we need to have a conversation about the truth behind the lies.

The truth in the lie

True to Nagle’s description, the temples of this cult of weakness – Facebook support groups, Tumblr, other networks – create an echo chamber of self-validating pain and vulnerability. This echo chamber is premised on an economy of reciprocity: because one would not want to be ‘invalidated,'[16] it is only too logical that one would have to validate everyone. There’s an undercurrent of hatred and skepticism towards anyone who challenges these self-identifications, be it disability status reviews, rude bystanders asking often insensitive questions, or indeed the medical profession, who are seen as dismissive towards the ‘disabled’ and the ‘vulnerable’, a fortiori where those conditions are concerned that evidence-based medicine does not recognize or does not diagnose with a frequency that would satisfy the echo chamber of pain. In this ‘safe space’, they are safe from the greatest threat to their chosen identity: reality.

Ironically, this claimed vulnerability is often counterposited by superficial and frequently excessive expressions of self-assurance and ‘toughness’: whether expressed often through radical political activism relishing in a tone of over-the-top vulgarity, a personal appearance and self-expression seeking to stand apart from culture even more (consider e.g. the ‘cripple punk’ aesthetic a manifestation of this dynamic) and the rhetoric of war and violence to describe disability and illness (such as self-descriptions as ‘fighters’ and ‘warriors’ at war against their health issues), there is a paradoxical display of exaggerated and situation-inappropriately presented strength. It is as if within the echoing walls of the temples of this this cult, its adherents are not quite sure whether to whisper or to yell, uncertain of who and what they are: strong or weak, heroic or vulnerable, victims or warriors. This is, of course, not unusual – many people this pertains to are at the age or stage of psychosocial development where their self-identity is still in the process of coalescing, and ‘trying on’ identities, even quite contradictory ones in rapid succession, is a normal part of that. But this paradoxical attitude suggests that something deeper is at play, that however willingly the role of weakness and vulnerability is adopted, it is at odds with other fundamental underlying impulses.

Following those underlying impulses and the odd complexity of strength and frailty at the same time, it becomes apparent that the young people in these echo chambers that Nagle is talking about are definitely not lying or misguided about one thing: they are in distress. They are broken and vulnerable. They are broken and vulnerable products of a society and an educational system that left them in a state of anomie that in and of itself could and should merit a psychiatric diagnosis. They are desperately looking for roles in this society, and the cult of suffering is the only one that has openings for them. They are suffering from a lack of having the mere opportunity to build something to be proud of, to try themselves against the tallest mountains, to explore, to fight, to lose, to win, to get the odd bloody nose and yet come home grinning from ear to ear, with the pride that comes from accomplishment. They may not have the thirty-something psychiatric diagnoses and fifty-odd chronic conditions they claim (if you think those numbers are exaggerated, you should go on Tumblr!), but they are experiencing legitimate anguish, and claiming the roles of weakness and vulnerability is their idiom of distress; the distress of their betrayal by a society that never gave them the chance to be anything but the roles of weakness and vulnerability they ended up adopting.

And we need to help them in finding a more fulfilling part in a more rewarding play.

References   [ + ]

1. Nagle, A. (2017). Kill All Normies: Online culture wars from 4chan and Tumblr to Trump and the alt-right. Zero Books.
2. Note I am not calling these matters unworthy of scholarship, merely admitting it is outside my experience and understanding.
3. Sophocles deals with that story in Trachinae, a heart-rending tragedy in its own right, and one I hope to return to in a future post.
4. All translations are by Doerries, B. (2015). All That You’ve Seen Here Is God: New versions of four Greek tragedies. Random House.
5. And his abandonment in turn caused a sort of reversion to a primal hunter-gatherer existence. Sophocles shows Philoctetes, a once-proud warrior and a civilized man, degraded to the point of a barbarian’s existence. In a sense, Philoctetes the Greek is dead, and all that is left is a husk driven by the most primal of human needs – food and water -, existing apart from society, apart from his people, apart from the polity. There was a particular degree of disgrace that came with such an existence that was easier to understand for a Greek audience than it is today.
6. I have an inexhaustible supply of crude, horrid and extremely tasteless jokes about sickness, in particular cancer, that I entirely credit the old guys at the hospital with. Nothing makes chemo fun, but listening to some seventy-somethings make the kind of jokes that people only make if they’ve seen heaven and hell was definitely a unique experience. They were also all kinds of loopy on their fentanyl pumps, so that helped. Someday I might write a post about this, but suffice to say that even serious illness is not all doom and gloom if there are people to share it with.
7. He turned out ok. After a brief bout of anxiety, he continued to improve. He is now a postgraduate student, and we still keep in touch. He has explicitly consented to me telling his story.
8. Data from NIH Genetics Home Reference.
9. Henter, J.I. et al. (1991). Incidence in Sweden and clinical features of familial hemophagocytic lymphohistiocytosis. Acta Paediatr Scand. 80(4):428-435. Cf. also Janka, G.E. (2012). Familiar and acquired haemophagocytic lymphohistiocytosis. Annu Rev Med. 63:233-246.
10. Defined in the US as any disease affecting fewer than 200,000 people US-wide – or roughly 1:1,500 people, while in the EU, rare diseases are defined as those with an incidence of fewer than 1:2,000 cases that are also life-threatening, chronically debilitating or inadequately treatable
11. In Tragedy and Civilization, a volume focusing on an interpretation of Sophocles, the author, Charles Segal, points out this peculiar coexistence of bloodthirsty savagery and high civilization in Ancient Greece in the book’s first, striking paragraph:

“High on a mountainside in a rugged and lonely part of Arcadia stands a remote shrine to Zeus Lykaios, Wolf Zeus. Plato alludes to a legend that human sacrifice was regularly practiced there, and the celebrant who partook of the flesh turned into a wolf. Across the valley from this grim precinct, in a spot of wild and desolate beauty, in a place known as the “glens”, Bassai, a small Greek city erected an elaborate temple to the most civilized of its gods, Apollo Epikurious, theHelper. Approaching this temple at Bassae from the city of Phigaleia, as the ancients did, the visitor experiences a striking visual confrontation of civilization and savagery. Before the ancient spectator stood the ordered geometry of columns and pediment outlined against the jagged mountaintops which stretch far into the distance. Freestanding and unexpected in that desolate setting, the temple seems an arbitrary example of pure form and human design as an attic amphora or the rhythm of a tragic chorus. But prominent just beyond the temple is the mountain where a grisly and primitive cult violated one of the first laws of human civilization as the Greeks defined it, the taboo against cannibalism.

12. Martinez, E. (1993). Beyond Black/White: The racisms of our time. Social Justice, 20(51-52), 22-34.
13. Note, for clarity’s sake: I am not alleging that the people referred to as part of this ‘cult of suffering, weakness and vulnerability’ suffer from FII or any related trait. I mention FII as it also manifests as a desire not merely of compassion and the sick role but also of the overcomer role. I’m also not making any assertions about how many of these people are actually sick, how many have a different disorder from what they’re claiming, how many are somatising/suffering from conversion disorder and how many are perfectly healthy and suffering from FII or just making stuff up. That is a question for medics. I’m looking at the diagnosis of the civilisational illness involved here, and for that, that’s all irrelevant.
14. At this point, it’s important to note the difference between the negative obligation not to emotionally harm a child intentionally, and the positive obligation to always emotionally foster and support children. There is never any excuse, by anyone, teacher or parent or coach, to intentionally emotionally humiliate a child. I’ve been there, and I know what it feels like, and I know that it’s the product of an inability to deal with one’s own insecurities as an adult, but that doesn’t justify it. It’s never OK. At the same time, nobody is responsible for your emotional wellbeing, and the idea that the world owes children a sphere where their precious self-esteem is never questioned and always positively affirmed is the worst preparation we can give to a generation facing the kinds of challenges our children do.
15. Although just how merciless that is has changed over the years. Especially with regard to physical fitness scores.
16. The ultimate sin on Tumblr, and roughly corresponding to any conduct that is not 100% affirmative of what one person believes is true about themselves, no matter how (un)realistic. While often criticized or sharply parodied, the insistence on validation and fear of/aggressive responses to – real or perceived – invalidation is an important mythopoetic act: it primarily serves to delineate and defend the community and the space in which the community’s cult, or ‘rituals’, are carried out. In a sense, it is akin to the markings on the trees of the sacred grove, bidding outsiders to stay out, or the various features that delineate a ritual space – an altar, or even an entire church, synagogue or mosque – from common spaces.

“Yeah, but what is it you actually DO?” A friendly explainer.

People ask me what I do a lot. I used to say “I work with computers”, but I realized this would earn me an invite to check out broken routers or messed up Outlook installations. Sometimes, I told people I was an epidemiologist, and a few insisted on asking me about skin disorders (err no… that’s dermatology). And eventually, in my exasperation, I asked around on our computational epidemiology mailing list how others deal with this question.

What you can expect next time you’re flying if you’re too specific about your research interests. That, or a spot on the no-fly list.

Turns out there’s no good answer. And I mean that, to the point that some people would rather actually check on Aunt Velma’s busted router. “Public health worker” sounds like a social worker. “I’m a mathematician that’s interested in diseases” strikes people as weird at best. And “Oh… I’m into ebola and stuff” gets you on the no-fly list faster than you can say Elizabethkingia.

If we’re lucky, your audience will politely nod once told what you do, and if we’re super lucky, they might google it later on. That you’re looking at this website may mean one of four things:

  1. You might be that exceptional lady or gentleman who did meet a computational epidemiologist, who handed you this link. Yay! You keep good company.
  2. You may have heard of what we do – or that we even exist – for the first time. Excellent! The longest journey begins with a single step. Or so the fortune cookie from last night’s Mama Chang’s says.
  3. You’ve been told you’re going to work with one of us, and you’re like ‘a whut?’. Cool! We’re a rare and endangered species, so please don’t shoot us.
  4. You’ve been considering, or you’ve been voluntold,[1] to go into the computational epidemiology field. That’s because you’re either an epidemiologist who is a bit of a geek or a geek who has a penchant for epidemiology. Welcome!

In the following, we’ll go over some of the basics of who we aren’t, what we do and how to care for your friendly neighbourhood computational epidemiologist, including some basic do’s and don’ts. With adequate care, your computational epidemiologist may live a long, happy life only occasionally punctuated by swearing at the command line. Let’s get started!

Who we aren’t

To get this out of the way: computational epidemiologists are NOT infectious disease doctors (in fact, despite the name, epidemiology deals with all sorts of illnesses, including non-infectious ones!), most don’t have an MD, and no, most of us never wanted to be doctors. It’s not where ‘doctors who couldn’t hack it go’. That’s naturopathic medicine you’re thinking of.

While statistically, ugly sweaters are more prevalent among computationalists, Kate Winslet’s character in Contagion (2011) is actually a regular field epidemiologist. We know that because she dies. Computational epidemiologists are presumably immortal.

We’re also, mostly, not field workers. Remember that movie where somebody brings home some zoonotic meningitis/flu hybrid from South East Asia and the whole world starts dying, and Kate Winslet plays an EIS officer? Well, while technically there are computationalists who do end up in the EIS, most of us prefer our subjects of study to be as far away from us as possible. Given that I study filoviridae in particular and their transmission dynamics in various simulated populations, I’m rather glad I can do so without ever having to see a filovirus. Not saying they’re not pretty (they do have their own kind of beauty), but I’d rather keep my distance from things that dissolve your cells, turn you into sludge and make you bleed out of orifices you didn’t know you could bleed out of.

This transmission network of tuberculosis was done on the basis of contact tracing data. We rely on field epidemiologists to get us that data so that we can then understand spread and risk factors better.
Source: Bjorn-Mortensen et al., 2017.

We do, however, depend on field workers quite a bit – all the nice graph models we look at began life as a bunch of scared graduate students in Tyvek suits sweating their butt off and in laboured French/English/Swahili/Igbo/other language tried to ascertain whom the sickly-looking gentleman in the corner of the room has been in contact with over the last few weeks (that’s called ‘contact tracing’, and is one of the most indispensable yet one of the most tiresome parts of field epidemiology).

We’re also not infectious disease biologists, although if you’re really interested in how to create one that will kill a lot of people, ask a computational epidemiologist. They won’t answer, because you look shifty and anyone who asks questions like that shouldn’t know anyway, but we’re the ones to know.

What we actually do

An early triumph of geospatial methods in epidemiology: John Snow’s cholera map.

We’re in a somewhat ill-defined field. At the margins, we touch mathematics, statistics, bioinformatics, computer science and computability theory, genomics, medicine, public health and probably a dozen other fields I forgot about. Ultimately, the core of what we do is using (and improving and developing) computational methods to answer complex questions about health and sickness.

One surprising aspect when I talk to people is that we’re actually not only working with infectious diseases. I was bitten by the epidemiology bug[2] when working on a Britain-wide project on predictive factors of heart disease. Epidemiologists also deal with obesity, drug use, workplace accidents and toxic exposure, radiation leaks and pretty much anything that can make you sick.[3]

The name does suggest an association with epidemics, but its roots are actually worth considering. Epidemiology is the art/science (logos) of what is ‘on’ (epi) the people (demos) – that is, the study of what has befallen the people. And an epidemic, of course, is something that befalls enough people that it might be worth considering as a population level phenomenon. The Greeks knew their thing when it came to naming stuff, and in a sense, this is brilliant naming, for it points out exactly what the great strength and the great weakness of epidemiology is: epidemiology is ‘good’ at answering questions about what’s going on with an entire population. It is notoriously less good at answering questions about what’s going on with an individual.

And so, when you tell an epidemiologist you have a sore throat, enlarged lymph nodes and a fever, they’ll tell you that statistically, you probably have acute bacterial pharyngitis caused by group A beta-hemolytic Streptococcus, aka ‘strep throat’. But statistically, you may also have infectious mononucleosis or lymphoma. That’s because if you look at a million patients with a sore throat, enlarged lymph nodes and a fever, most will indeed have acute bacterial pharyngitis (and most of those where a cause can be identified will have GABHS bacterial pharyngitis),[4] and the rest will have an odd smattering of cases. Because on a population level, every patient is a Schrödinger’s Cat: until they get conclusively diagnosed, they have 80% bacterial pharyngitis, 15% mono, 3% lymphoma and 2% some weird bug the lab sees once a decade.[5]

The power of this kind of analysis becomes apparent when we do need to deal with a population at large rather than a small number of individual patients. This is the domain of public health, and that’s why epidemiologists and public health physicians are best of buddies.

Consider the following scenario. Every once in a while, someone is unintentionally exposed to HIV, the pathogen that causes AIDS. In some cases, a regimen of antiviral drugs administered right after the exposure (known as post-exposure prophylaxis or PEP) can reduce the likelihood of HIV remaining in the system and developing AIDS. However, the antivirals in PEP are both expensive and, well, fairly nasty drugs, with their own side effect profile. Should PEP be routinely offered? And for how long?

Enter epidemiology to save the day and answer the question. Based on studies about the likelihood that PEP will prevent seroconversion (being infected by HIV), studies about the per-thousand-doses risk of the antivirals used for PEP, data about PEP’s effectiveness and so on, a more coherent statistical picture can be constructed. This allows for the quantification of risks vs benefits in light of effectiveness and efficiency. Epidemiology can answer questions that literally save lives every day. It factors into individual health and treatment decisions, into the guidelines that govern care and into public health policies, such as the availability of neuraminidase inhibitors[6] in a flu epidemic. It governs emergency responses, such as whether to respond to an outbreak by mass vaccination, ring vaccination, antivirals, isolation, quarantine or other measures. Ultimately, epidemiology is the art and science of using data to help physicians, public health officials and clinicians make the right decisions based on the right data.

The computational part

There are lots of ways to categorise epidemiologists (and none of them will be encountered with much favour – we like being uncategorised, thanks!). Sometimes, epidemiologists are categorized by the disease area examined (e.g. oncoepidemiology or psychiatric epidemiology), by patient group (such as pediatric or perinatal epidemiology or geriatric epidemiology), disease type epidemiology (in particular, chronic illness epidemiology) and finally, categories that look at particular methods of epidemiological research. Molecular and genetic/genomic epidemiology, for instance, looks at the genetic correlates of sickness and health, and what genetic factors determine or predispose to particular conditions – or the lack thereof. Much of this is using association studies – studies in which medical histories and genotyping are correlated to determine what factors are most strongly associated with a particular outcome.[7] Computational approaches are just another methodological category.

So what sets computationalists like me apart? We are concerned with using computational efficiency and mathematically efficient methods to deliver results. Our quest is no different from other epidemiologists, but our arsenal of tools is different. By using a combination of statistical, machine learning, geospatial, graph based and simulational tools (and whatever else we found in the kitchen sink), we can provide more accurate and detailed data to provide answers to questions that can prolong life, avoid side effects, alleviate suffering and help people live longer, healthier, more fulfilling lives.

Computational epidemiology grew out of the increasing digitization of health data – the volume of detailed health information in electronic medical records are a tremendous resource – and the rapid growth in high performance computational methods over the last few decades. The reason computational epidemiologists are trained in a uniquely interdisciplinary fashion, and are expected to be conversant with anything from linear algebra to graph theory, efficient tensor algorithm programming to computationally solving differential equations, from filoviridae to predicting zoonotic vectors, from modeling the spread of waterborne infections to mining Facebook – in short, just about anything and everything – is to be able to carry a toolbox as extensive as possible to tackle the widest range of challenges. Ultimately, we rarely encounter the same issue twice, and the ability to solve problems often has to do with combining the right tools in the right constellation for the job.

The future

Computational epidemiology is a new profession, and yet every now and then, I get asked whether new developments in technology will make us someday obsolete.

No doubt there have been a lot of new developments in various fields of computer science and mathematics has given us some new tools to tackle challenges faster and better:

  • Social networks provide a volume of data about individuals that together may predict disease trends, and web-scale databases can efficiently analyze it. An example of this is Google Flu, which uses search terms for flu-related concepts – things one with influenza-like illness would search for, such as ‘is it normal to use more than 250 tissues a day?’ – to gauge and estimate the expected disease severity in a particular region. The efficacy of Google Flu is controversial,[8] but the approach is definitely one that has a future. Efficient web crawling is another aspect of this.
  • Natural language processing helps analysing and interpreting unstructured, verbal information and allow analyses from unstructured data, such as news items or social media comments. NLP needs a lot of work as it currently stands, including the ability to understand non-literal language – irony, metaphor, etc.[9] -, but it has gone an enormous way over the last decades and has become a workhorse of analysing medical and social data.
  • Machine learning is a wide field, and it’s without doubt that the rising ML tide lifts our boats, too. Deep learning, for instance, has made levels of large genomic association studies (genome-wide association studies, GWASs) with thousands or even millions of dimensions possible[10] that hitherto would have required vast computing power reserved only to a few major institutions.
  • GPU based processing, together with the liberalization of access to computing power (consider AWS’s EC2 or Microsoft Azure), has opened up computationally intensive tasks to millions, and reduced the barriers of entry immensely by allowing pay-by-use instead of a massive upfront investment. The effect of this on our work cannot be underestimated.
  • The recent developments in synthetic populations and large agent-based models have made simulations of massive numbers of people based on real population data possible. This is an incredible opportunity, as it allows simulations to be conducted with a statistically representative communication while safeguarding patient privacy. Agent-based models are enormously useful not only to predict but to test potential interventional scenarios.
  • Graph databases can ‘organically’ represent relationship data, such as traced contacts. The result is the ability to perform searches (known as traversal in graph analysis lingo) over large networks in less time.
  • Optimisation and algorithmic research, in particular trying to parallelise as many problems as possible, is accelerating what we do every day.

But in the end, most epidemiologists find their strength and resilience in the fact that they are helping other humans live better, healthier lives. Unlike clinicians and field epidemiologists, we may not meet individual patients too often. But at the end of the day, behind all the numbers is a shared endeavor by a massive web of interdependent professions, from clinicians through pharmacologists and lab techs to public health workers and us computational epidemiologists to help people, to make their lives healthier and to alleviate suffering. It’s why we pull the crazy hours. It’s why we spend long days away from those we love. It’s what keeps us going after failed simulation #889982984234. And I doubt any algorithm, AI or robot, however advanced, can find that in their hearts.

While a lot of what’s in this post is important and factually true, the tone is occasionally a little more tongue in cheek than you might be used to on this blog. This is a profession for the slightly insane. Talking about it without a degree of self-deprecating irony is as pointless as it’s impossible.

References   [ + ]

1. Volunteering a la 12 Monkeys: “you, you and you!”.
2. That’s a metaphor. Epidemiologists are not made by insect bite, that’s Spider-Man. Epidemiologists are made, usually in small batches (use non-stick baking parchment and keep temperature below 250ºF). The process of creating decent epidemiologists has been engraved on the handle of John Snow’s pump. It hasn’t been seen since the 1854 London Cholera outbreak, sadly, so most of us have been winging it. Don’t complain, you’re still alive, right?
3. Controversially, this includes gun violence. Not to get into this fray, but epidemiology has neither the right tools nor the right approach to approach the tragedy of accidental and avoidable gun deaths and even less so for intentional and non-avoidable gun deaths. At some point, I’ll rant a little about how a lot of this has to do with the fact that when research money is at stake, everything looks like the kind of nail eminently suited for smashing by the hammer your working group came up with. Until then, I’ll stay quiet and try not to piss off too many people.
4. Note that because we don’t really bother with pharyngitis if it does the polite thing and goes away eventually, the definite cause of about a third of all cases of pharyngitis is never discovered. To put it in perspective: as the most frequent single pathogen causing bacterial pharyngitis, GABHS accounts for about 20% of all cases where the cause is known – in other words, ‘no known cause’ is still almost three times as frequent as the most frequent known bacterial cause!
5. These are not the real numbers, but you get the point.
6. Such as oseltamivir (Tamiflu), zanamivir (Relenza) and laninamivir (Inavir), used in the treatment of symptomatic influenza A and B infections. Controversially, their effectiveness is somewhat limited – at most, they cut off a few days off the disease length and for normal healthy patients, they may not make much of a difference -, but have pronounced side effects, some of which long outlast administration. At this point, meta-analyses show that in otherwise healthy patients, neuraminidase inhibitors do not have a favourable risk/benefit ratio.
7. A famous example is the case of PCSK9, a gene coding for a protein involved in lipoprotein homeostasis, which in turn is strongly correlated with heart disease and cardiac mortality. In familial hypercholesterolaemia, a heritable condition where people present with high cholesterol levels largely regardless of diet, a gain-of-function mutation of the PCSK9 protein is present. It was found that reducing the levels of PCSK9, such as by a targeted antibody that binds PCSK9 (the monoclonal antibodies evolocumab and alirocumab, for example), would reduce LDL (low density lipoprotein or ‘bad cholesterol’) and thus have cardiac benefits. In the end, so far, the effect has been quite modest compared to the exorbitant price tag, considering the much lower cost of statins that accomplish, more or less, the same purpose.
8. For a good summary, see Lazer, D., Kennedy, R., King, G., & Vespignani, A. (2014). The parable of Google Flu: traps in big data analysis. Science, 343(6176), 1203-1205.
9. Reyes, A., Rosso, P., & Buscaldi, D. (2012). From humor recognition to irony detection: The figurative language of social media. Data & Knowledge Engineering, (74)1-12.
10. Szymczak, S., Biernacka, J. M., Cordell, H. J., González‐Recio, O., König, I. R., Zhang, H., & Sun, Y. V. (2009). Machine learning in genome‐wide association studies. Genetic epidemiology, 33(S1).