Novichock detection and the Salisbury tourists

Image credit: EU Today.

The Salisbury novichok poisonings are a real can of worms. Media coverage is obviously politically, rather than scientifically, driven. Social and mass media reporting is highly partisan and the scientific components and reports (which are mostly classified) can become slaves to the particular political masters. I find the whole drama a mystery and certainly do not want to tie myself to any of the conspiracy theories, official or otherwise, that are floating around. It’s probably a subject to keep well away from.

However, one aspect intrigues me – the claimed identification of novichock residues in the London hotel room used by the Russian duo, Alexander Petrov and Ruslan Boshirov. In particular, is the identification of the material reliable and, further, is the reporting of this identification factual and reliable?

Media reporting: This generally assumes a positive identification, although at trace levels. The Sun, for example, reported:

“Petrov and Boshirov stayed in the City Stay Hotel in Bow, East London, during their time in the UK.

Cops searching their room two months later on May 4 are said to have discovered minute traces of Novichok, a high-grade military nerve agent created by Soviet scientists.”

And later:

“police found traces of Novichok in the hotel room in which the pair stayed for two nights.”

Similarly, the Independent reported:

“Investigators later found traces of novichok in their room at the City Stay Hotel.

They said the amount was too low to present a health risk but are appealing for any hotel guests who stayed there between 4 March and 4 May to contact investigators.”

Since Petrov and Boshirov surfaced and were interviewed the media coverage has become even more partisan and the discovery of these traces of novichock is being portrayed as even more definite.

The police reportIn the absence of an official scientific report of the analyses this is the best we have to go on:

“On 4 May 2018, tests were carried out in the hotel room where the suspects had stayed. A number of samples were tested at DSTL at Porton Down. Two swabs showed contamination of Novichok at levels below that which would cause concern for public health. A decision was made to take further samples from the room as a precautionary measure, including in the same areas originally tested, and all results came back negative. We believe the first process of taking swabs removed the contamination, so low were the traces of Novichok in the room.

Following these tests, experts deemed the room was safe and that it posed no risk to the public.”

This raises more questions, for the scientifically inclined, than the answers, seemingly, provided:

  • How many samples were taken – 2 positives is probably a low proportion of the total measurements?
  • Where were the sample sites located in the room
  • How do the low levels reported compare with the detection limits for the methods used?
  • Was the decision to take further samples based on lack of confidence in the results form the first sampling?
  • Again, how many further samples were taken and from what sites in the room?

I suspect that the two positive detections were probably false positives which the analyst had low confidence in. It is likely many samples were taken from the room so that two positives near, or at, the level of detection is not a good result. I suspect experts would challenge this evidence in court.

Absence of evidence is not proof of innocence

I should stress that in questioning the results I am not trying to argue for the innocence of the two guys. After all, a true professional would not have contaminated the hotel room. If the evidence is genuine, though, it may be more suggestive of a non-professional or non-state actor than a professional hitman.

The problem, though, at this stage is that all the other evidence made public is circumstantial and unlikely to stand up in court. The claimed positive detection of novichock-type compounds in the hotel room could be the key to a successful conviction so any doubts should be removed.

Novichock compounds

The following presents my views on the problems of detecting novichock compounds at low levels and why I think we should not accept the current media reports as positive evidence. A court would have to look very critically at the actual data and detection methods used. At the moment the political and police statements could be expressing far more confidence in the reported findings than is actually warranted by the real evidence.

An Iranian paper from two years ago, Hosseini et al., (2016) provides information on the synthesis, structure and detection of novichock-type compounds. It is probably the most up-to-date information publicly available and its citation is

Hosseini, S. E., Saeidian, H., Amozadeh, A., Naseri, M. T., & Babri, M. (2016). Fragmentation pathways and structural characterization of organophosphorus compounds related to the Chemical Weapons Convention by electron ionization and electrospray ionization tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 30(24), 2585–2593.

The paper describes the micro-synthesis of two compounds that are listed under Schedule 2.B.04 of the Chemical Weapons Convention. These are:

  • Compound 3: N-[Bis(dimethylamino)methylidene]-P-methylphosphonamidic fluoride, and
  • Compound 4: O-alkyl N-[bis(dimethylamino)-
    methylidene]-P-methylphosphonamidate Novichok derivatives

The figure shows the chemical structures of these compounds.

The F atom in compound 3 is replaced by an organic group (R) to form the novichok derivative. As this can be either of a wide range of organic groups (the authors list nine different groups for derivatives they synthesised) the novichock-type compounds include a range of different chemicals with differing levels of toxicity.

This is why more official reports on the Salisbury poisonings refer to novichock-type nerve agents and not just novichock.

Before any clever reader decides to use this paper to synthesize their own samples of these or similar compounds I must stress the warning provided by the authors:

“It should be noted that, due to the extreme toxicity of these materials, the separation and purification of CWC-related chemical are very difficult and therefore should be carried out only by a trained professional in an efficient fume cupboard equipped with an active charcoal filtration system.”

Detection of novichok-type compounds

Mass spectrometry methods are used for detection. This involves breaking up the molecules into fragments using an electron ionizer (EI). These molecular fragments are then separated according to mass and charge and the amounts of each detected in a mass spectrometer (MS) to produce an EI-MS spectrum.

Each compound has its own “fingerprint” – a pattern of peaks defined by the mass/charge (m/z) of each molecular fragment and the relative intensity of each peak. The figure below shows the EI-MS “fingerprints” for compound 3 and the O-ethyl derivative of compound 4.

We can see why the detection of a compound relies not only on a single peak but also other characteristic peaks and their relative sizes.

For example, the largest peak (H) at m/z = 71 occurs in both compounds. This is because the molecular fragment (see the chemical structure to the right) responsible for it is produced by ionization of both compounds. So that peak cannot be used alone to differentiate between the two compounds. Identification of a specific compound requires locating all the major characteristic peaks and ensuring their relative intensities are correct.

This is straightforward where the compounds are available at relatively high concentrations and the combination of mass spectroscopy with gas or liquid chromatography helps to remove some of the background chemicals. The ability of UK experts to conclude that the type of novichok used to poison the Skripals is the same as that in the fake scent bottle used by the second victims (Dawn Sturgess and Charlie Rowley) means that they were able to recover samples containing the nerve agent at sufficiently high concentrations.

But, at low concentrations one may simply not be able to find all the characteristic peaks, and identification using just the most intense peaks is not so reliable. For example, compounds 3 and 4 could not have been differentiated at low concentrations if all that could be detected were very small peaks at m/z =  71, 135 and 150. Yet that is the situation when searching for trace levels and one is always conscious that the peaks that are detected could be due to low levels of a completely different compound.

Conclusions

I suspect the description of the two possibly positive samples in the London Hotel as trace levels or “at levels below that which would cause concern for public health” were interpretations driven by “wishful thinking” and exaggerated confidence and not surety. After all, scientists often face such pressures when their political masters are looking for results to fit a preconceived narrative. It is easy to be persuaded in such situations. And it is tempting for both scientists and police to describe their findings in a more confident way when presenting to the media than they would during peer discussions in the laboratory or office.

My suspicions are supported by the fact that the total number samples taken from this hotel room must have been quite large so that makes the reliability of the positive values at such low levels for only two samples quite suspect (although information on locations of sampling sites would help this interpretation).

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22 responses to “Novichock detection and the Salisbury tourists

  1. Thanks for that
    I also thought that an initial false positive was more realistic than the original swabbings having dispatched all sign of novichok
    Its rather disturbing that the media now seems to be a complete tool of foreign policy agendas, airing opinions and “evidence” that the authorities could later be found culpable for
    Mind you, I think this was probably always the case, but these days they don’t even put much effort in . It’s insulting!
    Or most people are too busy keeping their heads above water and find compliance and belief easier than doubt. I find my younger friends really don’t want to engage with this stuff, and just go along with the TV versions, whereas my retired friends have the leisure (finally) to investigate further.
    I seriously wonder if NZ today would have the balls to declare itself nuclear free.
    Thanks for providing a science based critical look at the allegations, you do great work, and I’m much obliged

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  2. By the way do you mind if I link to your posts on the various sites I visit?

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  3. Christopher Atkinson

    I am curious how even a small quantity of this extremely dangerous substance could possibly leave trace amounts?

    Even the most inept ‘hitman’ would use a container designed to prevent release of even the minute amounts?

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  4. Neither the chemical name, chemical structure or chemical family of the Salisbury or Amesbury substances have ever been officially released. “A Novichok” can refer to any substance investigated or developed by the Russian military after the 1950’s but sometime before 1994. It’s premature to narrow the potential substances down to just those you have mentioned. It’s well documented that the Russian’s investigated all sorts of substances, including for example, first strike incapacitant’s, like fentanyl’s, and specifically carfentanil. Indeed, Porton Down published a paper in 2012 making exactly the same point with regards to the incapacitating chemicals deployed by Russian special forces to end the Moscow Theater Siege.

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  5. Go for it reenmac.

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  6. Thanks for the more scientific angle.

    So much for the deadliness of Novichock. With so many survivors, the time has come to relabel it and refer to it as ‘Novichokolate.’

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  7. “Two swabs showed contamination of Novichok at levels below that which would cause concern for public health”

    I thinking now, when would it become a concern to public health? There are acceptable levels? Have I missed something?

    ps why does my identicon look like a Novichok molecule?

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  8. Good questions, Ken. Here’s another:

    Why was the MET police disinterested in adding to the flimsy evidence for their ‘novichok hotel’ case – why did they not immediately track down all later occupants of the hotel room Petrov and Boshirov stayed in, and take swabs of their suitcases and/or other belongings?

    When it comes to looking after the public they can possibly (and tenuously) get away with the “well, nobody is reported to have been affected” argument, but when it comes to the INVESTIGATION aspect, I’d like to hear an explanation for the failure to investigate.

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  9. Max, it is hard to know what is official for the UK. Certainly, most of the political statements and media statements are so partisan that one cannot consider them thought out.

    However, the legal consideration of taking blood samples from the Skripals for the OPCW did receive testimony which referred to novichok-like or novichok-type compounds having been detected.

    For the life of me, I cannot understand why the UK has classified the OPCW report on their findings in this case, or why the summary of their report (which was declassified) does not actually describe the name and structure of the compounds identified.

    So, yes there is plenty of room for speculation – although I suspect that because analysts have conveyed information to the police and government and they are using the novichok terminology that the compound identified is one of this group.

    The hesitancy of naming the actual compound and the classification of scientific reports which might do so might be hiding the fact that the identified compound is one of the less toxic ones.

    However, my comments about the difficulty of identifying any compound at such low concentrations still stand. As does my belief that reading between the lines the analysts involved probably consider the two positive readings as false positives.

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  10. Excellent article. I would suspect that the lab would have a Limit of Detection, and a higher Limit of Quantitation. If the samples showed parent ion and fragment ions which permitted a search and a “hit” but were below the LOQ then that might be how we got to where we are.
    Or Porton Down are making this up as they go along, and Novichok in the hotel room is actually the only “evidence” linking the two Russians to the Skripal attack.
    The door knob application of a gel with an atomiser is flawed.

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  11. Well if we’re speculating…

    I’d suspect that you are probably mistaken that any chemical from the group you have mentioned was involved in the Salisbury incident.

    One needs to take all the evidence available into account…

    As an example, the same substance in a pure form was also found 4 months later in a counterfeit perfume bottle with a modified long nozzle dispenser, on the kitchen worktop of Charlie Rowley’s new home. Charlie & Dawn were substance abusers, and Charlie is also a convicted drug dealer.

    As this 2015 Australian article shows, people have been smuggling illicit drugs by packaging them inside seemingly innocuous items for a long time…

    “Drugs are being concealed inside everything from perfume bottles and porcelain toilets to lava lamps and classic American muscle cars in a bid to feed Australia’s seemingly insatiable appetite for cocaine, ice and ecstasy.”

    https://www.smh.com.au/national/customs-pulls-back-the-curtain-on-the-weird-and-wacky-ways-drugs-are-smuggled-in-20150710-gi9mdi.html

    Since 2015 however, the type of drugs being smuggled have changed, there are all sorts of new designer drugs, and new synthetic opioids such as powerful fentanyl’s… they are the new kid on the block… Hundreds of different chemical structure versions of this compound are now available…

    https://edition.cnn.com/2018/05/25/health/nebraska-fentanyl-bust/index.html

    The modified dispenser on Charlie’s bottle just gives it away. As does his new home, suggesting his income had recently increased.

    There is very little doubt in my mind that the Skripal’s were somehow mixed up in illicit narcotics, and the Salisbury substance was one of those illicit narcotics, just as the hospital and the local police initially claimed in both the Salisbury, and Amesbury incidents.

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  12. @ Ken,

    I think you have answered your own question:

    “For the life of me, I cannot understand why the UK has classified the OPCW report on their findings in this case, or why the summary of their report (which was declassified) does not actually describe the name and structure of the compounds identified.”

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  13. Ken,

    If you’re suggesting that the hotel swab results were false positives, then that raises another question that you don’t seem to have considered.

    What proportion of swabs, taken from random hotel rooms worldwide, would you expect to test positive for novichok, or indeed any other military nerve agent?

    I agree that the public do not have access to all the evidence in this case, but you appear to be stretching the little evidence we have into areas best left to the conspiracy “theorists”.

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  14. Stuart, I think the information I have presented on the problems of detecting compounds like this at extremely low concentrations and the reasonable conclusion about the number of samples taken from that particular room does indicate I have considered this question.

    The number of positives from this room was very low (we can assume quite a large number of samples were taken) and the police statement (which is all we have to go on) does indicate a lack of confidence in these results.

    I would think a similar proportion of samples taken from hotel rooms anywhere in the world would provide a similar number of false positives (or perhaps even higher number considering the lack of control of insecticides etc in many countries).

    You agree there is a problem of evidence (and surely we are entitled to ask why in such a serious situation. Serious claims have been made but the UK authorities refuse to release the scientific evidence or allow the OPCW to release their results). But that is the very climate where conspiracy theories thrive.

    The biggest and most heavily promoted conspiracy theory is the one promoted by the UK government. In fact, it is that conspiracy theory which drove samples to be taken from that particular hotel room.

    But who is stretching the evidence? These two Russian men have been placed in the frame purely becuase of circumstantial evidence – many other tourists could have fallen victim to that situation. The only non-circumstantial evidence the police have to go on is extremely flimsy and I certainly do not think it would stand up to expert scrutiny in a court of law.

    I am not at all convinced by the UK official conspiracy theory (which is largely driven by racism) and certainly don’t adhere to any other (and there are a lot floating around). I am in the position of being happy to say “I don’t know.” But add that we are entitled to see the evidence the authorities claim they have considering how dangerous the situation is.

    Please note what I said in my introduction:

    “I find the whole drama a mystery and certainly do not want to tie myself to any of the conspiracy theories, official or otherwise, that are floating around. It’s probably a subject to keep well away from.”

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  15. Ken, I have concerns with your post. And these are concerns based on my experience of measuring minute amounts of organophosphates (part per billion down to part per trillion levels) in environmental samples using mass spectrometry. Old job, which I left because I couldn’t stand the animal studies.

    Understandably, you’re presenting a very unsophisticated discussion of mass spectrometry for organic analysis to a lay audience. But you’re falsely giving the impression that mass spectrometry is inadequate for trace detection. This could not be farther from the truth–and borders on lying.

    The discussion of “False Positives” is totally baseless, and can be ruled out easily using proper controls. It is certain that this was done: *NO* analysis is ever accepted, let alone its results shared outside the lab, without controls. Full stop.

    Electron Ionization is emphatically not the only method available. In fact, for identifying an unknown compound, it is only one of a few tools that would be used. It does give valuable information about fragmentation patterns, which with a bit of study can reveal structural motifs (and any good organic analytic chemist knows how to do this without consulting a database). The identity of those fragments can be further confirmed using tandem mass spectrometry. And if any uncertainty remains, likely compounds can be synthesized as references for comparison. Porton Down is more than equipped for this type of work.

    But EI is the definition of a “hard” ionization technique: one that may not reveal the complex, high molecular weight ions such as the parent ion (i.e.: the original structure). To do this, soft techniques such as Chemical Ionization or Laser Desorption Ionization can be used. With the exact mass in hand, the chemical formula can be determined unambiguously. *IN THIS CASE, IT IS SUFFICIENT TO RELY SOLELY ON THIS PEAK FOR DETERMINATION OF THE CHEMICAL FORMULA.* Structural details are not well-determined by soft ionization methods, but the combination of both EI with a Soft Method leaves very little room for doubt. And that little room is removed entirely if both agree with a reference material (further characterized by NMR, IR, Raman, etc.).

    I implore you to stop misleading your readers.

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  16. DDTea, of course, I am not claiming mass spectrometry is no good for trace detection – quite the opposite. I have no idea what gave you that impression.

    My inference that the two samples in question probably gave false positives was made from the facts around this case (as contained in the police report), not the methodology.

    1: Only two samples gave such positives – yet I would have expected a large number of samples to be taken from a hotel room. So probably a very small proportion of the total.
    2: Analysts appeared to have a low confidence in their finding because they resampled at a later date.
    3: The new samples were all negative, suggesting that the analysts were correct to feel unconfident about their earlier results.
    4: Given the political atmosphere every effort would have been made to find positive readings.

    Yes, it seems likely that other methods would have been used to check out those specific samples (again given the political atmosphere). Yes, I am sure Porton Down have their own samples of these compounds that could have been used as controls and checks. Despite the claims of the UK government it is unreasonable not to assume that laboratories like Porton Down do not keep supplies of such chemicals.

    The fact remains, that despite the availability of a range of methodologies the analysts could not replicate their original results. This does suggest they must have been operating near the detection limits.

    Of course, given that the UK has a habit of classifying anything of real value all we have to go on is a reasonable inference. In the absence of the objective reports, I think my inference is reasonable. It is misleading of you to imply I am not being honest when you ignore completely the factors leading me to make that inference. In fact, your reference to other techniques seems to be a diversion from the relevant facts.

    Perhaps you are the one attempting to mislead the readers.

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  17. DDTEA is most often featured on Bellingcat, a loyal servant to the Atlantic council, whose starting point in any investigation is “Russia Dunnit”
    I hope this stuff isn’t taking up too much of your time(though I’m very grateful for your clear responses)

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  18. Thanks for that information, reenmac.

    So the comment was clearly an attempt at diversion.

    Bellingcat and the Atlantic Council are hardly reliable sources in these matters. Unforuitantely I do not follow them closely enough to pick up the connection. But a little search shows this person spreading disinformation and diversions in Bellingcat about chemical weapons in Syria as well.

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  19. It’s plain that you are attempting to muddy the clear waters around the Russian government’s responsibility for the reckless release of an illegal, and internationally prohibited, chemical weapon in the UK:

    ” If the evidence is genuine, though, it may be more suggestive of a non-professional or non-state actor than a professional hitman.”

    See? Here you go trying to deflect blame from the GRU with defective logic. It doesn’t consider that state intelligence operatives really can be very sloppy. And based on experience with Russian and Soviet external operations, we *know* the GRU is very sloppy. So sloppy, their operatives leave the phone number of the Russian Defense Ministry in their passport applications.

    But addressing your other points, you’re fishing for suspicion.

    “1: Only two samples gave such positives – yet I would have expected a large number of samples to be taken from a hotel room. So probably a very small proportion of the total.”
    –Right. Because a larger leak, in multiple points, would likely have killed the suspects. This sounds like the investigators were very thorough to detect such a trace amount of material. And by the way, if they follow the usual swabbing method, they would have taken a blank swipe as well (i.e.: a negative control). As the police report mentioned, swabbing likely removed from contamination.

    “2: Analysts appeared to have a low confidence in their finding because they resampled at a later date.”
    –No, they probably went back to make sure the room was safe for the public or whether it would have to be decontaminated.

    “3: The new samples were all negative, suggesting that the analysts were correct to feel unconfident about their earlier results.”
    –Or, like the police report said, the earlier swab removed the contamination.

    “4: Given the political atmosphere every effort would have been made to find positive readings.”
    –Come on, this is just BS. That isn’t how these things work. No, we scientists do not, “face such pressures when their political masters are looking for results to fit a preconceived narrative.” We let our data guide our conclusions.

    I guarantee that there were no “false positives” involved anywhere given how easily these could be ruled out. If nerve agent was detected, then it was there.

    All the mass spec discussion about how some of the smaller masses couldn’t be detected is irrelevant. Not every fragment must be detected, just the high-value characteristic ones in the right proportions under the same experimental conditions. Talking about LOD’s and LOQ’s is just superfluous–they wouldn’t have reported a compound if they could not detect it.

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  20. Oh come on !
    If they were that sloppy, they would never have been allowed on the TV screens.They would have been “eliminated ” according to all the unnamed “security sources” the UK media trots out
    There are no certainties about this case.All this speculation would be avoided if the UK authorities released CCTV images of the Skripals on the day, or released the information they must have gained from questioning the Skripals
    .Far too much unwarranted secrecy and frankly ludicrous accounts of special doorknob swabbing techniques, and bold midday novichoc dousings,with the very real risk of being seen
    Why no actual interviews of the Skripals?
    Practised statements are really not the same
    Sorry, but your certainties are totally untested and unfounded

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  21. Christopher Atkinson

    DDTea,

    Enjoying the posts, however you do appear to be ‘working backwards from your conclusions’ –

    “Russian government’s responsibility for the reckless release of an illegal, and internationally prohibited, chemical weapon in the UK:”

    The obvious result is that the ‘evidence’ is fitted around the your bias/narrative

    I am intrigued what you think of Theresa May’s and Boris Johnson’s unequivocal international condemnation and accusations directed towards Russia long before any ‘evidence’ came to light?

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  22. Facebook has also deleted my post about this article. Wonder if this purge has anything to do with DDTea and his relationship with the Atlantic Council – Facebook’s “fact-checker?”

    Like

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