Monday, 29 August 2016

A pile of TWADALs...

During my few days chatting with a gaggle of hardcore vaccine denialists, I developed a term and acronym...TWADAL

The term stands for "Those Who Are Decided Against Learning", because those I engaged with were not "vaccine hesitant" in any sense. 

They were mostly dedicated to pushing an agenda of anti-science, anti-logic, anti-politeness underpinned by memes and quote-cards highlighting every rare bad outcome from a vaccine, every side (well known and mostly minor) adverse event and never once mentioning all the lives that vaccines have saved and protected yesterday, today and in the future. 

By all means describe this as name calling - but go spend some time engaging with TWADALs first - some quality time. Prove to me that they are open to learning anything new. Show me that after they drop into your social media neighbourhood unannounced and spew unsolicited, unverifiable out-of-context untruths about vaccines killing people, collect a few others to pile on, call you a shill for big pharma...that they will then concede any of their points when you try to engage them in a calm discussion. 


Sunday, 28 August 2016

Colombia Zika virus report, Epidemiological Week No. 33...

UPDATE No.1: 29AUG2016
The latest epidemiological report from Colombia, which includes data on Zika virus disease (ZVD; 14AUG2016-20AUG2016), has been produced by the Colombian National Institute for Health team.[1]
NOTE: While these data were reported the past epidemiological week, they may not be from that week. See earlier post about possible reporting lag.

Graph No.1. The cumulative curve of confirmed ZVD cases
(green circles, left-hand axis) and the change in confirmed ZVD case
numbers when compared to the preceding week's total
(green bars, right-hand axis). Data from [1].
Click on graph to enlarge.
Graph No. 1 shows that 0 new laboratory confirmed cases of ZVD were reported this week; the 6th week of this. The total sits at 8,826 or 9% of all clinically suspected Zika virus (ZIKV) detections.

Graph No.2. The cumulative curve of suspected ZVD cases
(pink circles, left-hand axis) and the change in suspected ZVD case
numbers when compared to the preceding week's total
(red bars, right-hand axis). Data from [1].
Click on graph to enlarge.
Graph No. 2 shows the change in suspected cases. These are not laboratory confirmed. The suspected ZVD cases continue to rise but have been slowing for weeks, adding 270 this week to total 93,551.

Graph No.3. The cumulative curve of clinically suspect (lilac triangles, left-hand axis) and confirmed ZIKV infections (lilac circles, left-hand axis) and the change in
confirmed ZIKV infection numbers when compared to the preceding week's total
(purple bars, right-hand axis). Now added the reported number of microcephaly cases
confirmed as ZIKV infected (yellow bars, right-hand axis). Data from [1].
Click on graph to enlarge.
Graph No. 3 shows that to epidemiological week (EW) No. 33, 11,752 suspected (+30 compared to last week) and 6,054 confirmed ZIKV infections (-2) have been identified in pregnant women.

As of this report, 34 (+5 from last EW) live births have been diagnosed with congenital ZIKV syndrome (CZVS; microcephaly/central nervous system disorder), confirmed as being ZIKV positive. That represents 0.53% of all confirmed ZIKV positive mothers-the 4th consecutive EW in which this proportion has risen.

Some back of napkin calculations looking at these numbers suggest that there are 5-6 deliveries for every 1,000 ZIKV-positive pregnant women that result in a ZIKV infected baby with microcephaly. This assumes each neonate has been tested for ZIKV as [6] suggests. This figure has no clear understanding of the number of aborted or miscarried foetuses that are also occurring from ZIKV-positive pregnant women. Abortions and miscarriages will need a local baseline to understand the scope of this component of the impact of ZIKV infection.

209 other microcephaly diagnoses (down from 254 last week) are now under investigation - this value has also been rising very quickly and suggests suspicious CZVS cases in Colombia are accruing faster than the pace of complete investigation can keep up with. 

It now seems very likely that we can expect those bars to keep rising steeply in the coming weeks. The line is well and truly crossed.

Graph No. 4 below focuses on just the ZIKV-positive cases and those that remain under investigation, highlighting how the investigatory total has changed each week and been trending upwards since Epidemiological Week No. 14 and rising by +5 for 2 weeks in a row.

Graph No.4. The change in confirmed ZIKV infection numbers
when detected in association with a microcephaly diagnosis, compared
to the preceding week's total (yellow bars, left-hand axis). Data are from [1].
Click on graph to enlarge.
It has now been 317 days, or 10 months 12 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[2] Colombia is currently carrying the next biggest load of suspected ZVD cases [8] (although more confirmed in Puerto Rico. NB: not all of the "Casos confirmados" are lab confirmed, but I'm told most are).[3] Keep in mind that when talking about microcephaly - we have to think back in time to what insult or infection might have occurred in the first or second trimester (probably-still not definitive). The counts of virus occurring this week will have zero impact on what happened back then. Also keep in mind that Colombia may be reporting things differently from Brazil.[5,7]

Brazil first reported positive (but unconfirmed) laboratory tests for Zika virus disease on 29th April 2015. Brazil then started to report a rise in foetal anomalies (an initial 141), in the form of microcephaly on 30th October 2015. This was 184 days - or about 6 months later.[4]


References...

  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/2016%20Boletin%20epidemiologico%20semana%2033.pdf
  2. http://www.who.int/bulletin/online_first/16-171082/en/
  3. http://www.nature.com/news/first-zika-linked-birth-defects-detected-in-colombia-1.19502
  4. http://who.int/bulletin/online_first/16-171082/en/
  5. http://virologydownunder.blogspot.com.au/2016/06/the-elephant-squeaked.html
  6. Zika Virus Disease in Colombia — Preliminary Reporthttp://www.nejm.org/doi/full/10.1056/NEJMoa1604037#t=article
  7. https://www.statnews.com/2016/06/22/zika-abortion-latin-america/
  8. http://www.salud.gov.pr/Estadisticas-Registros-y-Publicaciones/Pages/Informe-Arboviral.aspx
Updates...
  1. Clarified Puerto Rico has more confirmed cases than Colombia but fewer suspected

Friday, 26 August 2016

Get off my lawn you experts!

Two things were suggested by Richard P Grant in his recent piece for the Guardian, as reasons why scientists are losing the battle to communicate science.[1] 

First, scientists keep telling people how to live their lives and second, scientists don't listen to people.

Okay - I agree. Scientists do that. When I started on social media, I mentally added "try not to be a supercilious git" to my list of things to do to be a better human being. That was up there with "make memories for my kids", "always work at my marriage", "don't speak ill of other people", "listen instead of interrupting", "don't be unintentionally racist", "be conscious of innate bias"...the list goes on and keeps growing. 

But I still come across as a supercilious git on occasion. I'm not really sorry about that though. The main reason I do so is because my tribe is that of the scientist (#tribescience ?). A few different science tribes really. I've spent the past 30 years picking up the ways of my tribe - certain phrases, learning to speak in certain ways, using big scientific words, writing with a certain pattern, producing documents that everyone - including me - find boring, seeing patterns and thinking about how things around me can be tested, seeking out the next big idea that will fund my life and home loan and trying to remain agile enough to be prepared to update those views and words when all that I've learned changes in an instant. Imposter syndrome for an academic can drive the need to sound just as supercilious as our peers. It's a lot of baggage to set down if you dip in and out of interpreting science for the public. Facts, not excuses.

As a little experiment, I thought I'd look at how far listening got me when related to the "dangerous ones" [1]- the hardcore anti-vaccination believers. Not my first attempt to understand this group and not my last.

I'd already been in a small chat where someone @MaykeBriggs (not an anti-vaxxer let me stress) had suggested pesticides and "vaccine toxin" exposure should be looked at in relation to Zika virus and microcephaly in Brazil. I'd asked which toxins and we'd had a discussion about phenoxyethanol, used as a preservative in vaccines.[2,3] Interestingly, phenoxyethanol is used widely, because of its fragrant properties, in shampoos, toilet soaps, decorative cosmetics and is found naturally in avocado, endive and tea for example.[3] The things you learn when you read around a topic!

Example of anti-vax brochure.
Next I received a snippet of an abstract by tweet from @LaLaRueFrench75. This went back and forth and just before I went to sleep got a request to comment on a couple of slides of aggregated science and theory by @2ndfor1st. When I woke up I had more tweets awaiting my sultana bran breakfast than on any day during the worst of the Ebola virus event (which got pretty busy for me). 

I'd apparently inadvertently poked an anti-vaccine nest with a stick.

I Storified the whole thing if anyone wants to check it out. 

The biggest thing for me was, I couldn't have told this group how to live their lives even if I'd wanted to! There was no discussion to be engaged in-just me being shown their material from several tweeters at once. Attempts to correct obviously wrong material were ignored, shouted down or artfully sidestepped.

I took a few other things away from this:

  • These are not the vaccine hesitant [5] - people sitting on the fence about whether this or that vaccine may be good or bad for their child. These are fully engaged professional aggregators of content, curates into a story to support whichever thread they are interested in highlighting.
    This group create slick websites, videos, brochures and run a tight campaign to recruit like-minded followers and cast aspersions upon efforts to make our children even more healthy, reduce the burden of chronic disease and prolong life. 
  • A central theme seems to be that there is a conspiracy to force their children to be injured by vaccination, perhaps mostly in relation to mandated vaccination, but vaccines in general.
    But the community today could not show me any example of this injury. It has become a ethereal symbol for the movement, but there is no form nor substance to the claims of death or severe harm by vaccination.
  • If you choose to engage with this group, pick a particular point to address and do not let yourself be dragged away from it by the constant movement of goalposts you'll encounter. If you don't get the answer you're asking for, say that and move on.
  • If you are a scientist planning to engage the public - engage with this group. There is much to learn about communication and about yourself.
    You may be pilloried by your peers (psst - just don't tell them), but you may also gain important experience with extreme believers and very alternate viewpoints.
  • Those against using vaccines - at least based on my example - are mostly focused on the secondary ingredients especially preservatives and adjuvants - aluminium, phenoxyethanol, thiomersal.
    This is pretty low hanging fruit though, because there could be more scientific studies to address some of the questions asked. Science has made a rod for its own back here.
  • This group do have valid concerns. But instead of being able to believe or engage experts, they choose to actively decry them as the puppets of commercial interests and instead seek out words, sentences, clips and snippets to support their views about their concerns.
    Based on a lot of reading this past few days, this material is often "home made", out of context, quote studies that employ excessively high amounts of the chemical in question, or use the chemical repeatedly in a way that does not at all reflect vaccination, or use studies that do not have suitable control groups (h/t @JATetro).
  • The misuse of funds by medical doctors was also a big thing among this group. Apparently this extends to scientists - although that's laughable to me as I'm a science Doctor who has spent many years experiencing how hard it is to scrape together money to get to a conference let alone travel the globe in style.
    I'm aware of the conflict of interest issues pertaining to medical doctors being paid by pharmaceutical interests. The presumption today was clearly that these payments sway these evil doctors towards prescribing that company's products, including more use of vaccines.
    Oversight of vaccines both during early safety and subsequent clinical trials and when later while being monitored for adverse events once they are commercialised, requires experts to come together to review data (costly) - data which themselves are very expensive to collect and collate.
    These payments, must be transparently documented or else consumer trust is rightly shaken. 
  • Those who invent, develop, administer and oversee use of vaccines are seen as different
    "Them and us"
    humans from the true believer anti-vaxxers. This may be for ulterior motives or because of a past bad experience.
    The impression I got was that the  professionals are not thought of as having the same skin in the game - their own families, lives and children - as do "the public".
    Do some of our science and medical doctors need to humanise more, at least in this space?  
  • If you write about scientists who try and engage with the public, maybe think more deeply about the term "science communication". Currently it seems to cover everything that comes out of the mouth/keyboard of a scientist. Its too broad. How about adding some more terms? What about Science Interpretation? Science Engagement? If you paint all science communication as coming from a place of arrogance and control, you paint every scientist, even those who honestly try to do better, as arrogant and controlling.
    That's some poor research right there.
    It's also a tone that is likely to discourage other scientists out of their highly competitive, poorly funded, stressful, depressing, abusive, overcrowded, biased, "cosy little bubble and make an effort to reach people where they are, where they are confused and hurting; where the need"
Of course, if we do seek out people who seem confused, there is no guarantee we'll be able to get a word in edgewise. That does make being a tribal and supercilious git all the more challenging. But it's what we scientists excel out. Right?


References...

Saturday, 20 August 2016

Tests and temps...

From [10]
It's been about 5 weeks since Brazil updated its microcephaly-related-to-Zika-virus reporting index page. 

The last post listed (a couple of others made their way out via other channels) was from epidemiological week (EW) No. 26. 

For comparison, Colombia is about to post data for EW No. 32. [12]

Interestingly, Colombia's National Institute of Health has not seen any new laboratory confirmed Zika virus disease cases during that same period - so perhaps Brazil is not seeing any either?

Temperature graphs (in Celsius) from 
accuweather.com.
Top-Miami Beach, Florida.
Bottom-Rio de Janeiro, Brazil
Meanwhile, more of the US state of Florida is seeing local Zika virus spread.[4,5,6] If we look at the temperature graphs we can see that Miami Beach (around 32'C)  is certainly a lot warmer and holding more steady than Rio (around 24'C) in August 2916. 

High and fluctuating temperatures are important for flavivirus multiplication in mosquitoes but for the mosquitoes themselves, particularly Aedes aegypti, they can live for about the same period (around 3 weeks) when conditions suit, whether at 26'C or 30'C.[12,13]

As I was recently taught by Rebbeca C Christofferson and Anthony Willson, viral loads do better in mosquitoes living at an optimal temperature. But when more Dengue virus for example, is replicating throughout the mosquito, that can have an effect on the length of their lives, even if not having an immediate impact on mortality.[14]

When you stop and think about it there is a lot going on for a mosquito when it takes a big blood meal. 

There could be a huge rapid weight gain, and there can be a 20'C temperature difference between the host's blood and the insect's temperature - that's a big shock at any size! There is also a big osmotic imbalance (difference in osmotic pressure due to the concentration of dissolved solids in the host's blood versus that in the insect's hemolymph [8,9]) and there's a need to get rid of toxic metabolites.[1] 

Have you seen that big drop of excreted fluid attached to some species of mosquito's butt? It appears once feeding has started and is something they excrete (urine and concentrated red blood cells; a process called prediuresis) to help them balance osmolarity, offset weight gain and sometimes to regulate their temperature through evaporation.[2,7] 

Some mosquito species retain the drop ('drop-keeping') making use of evaporative cooling, some emit new drops.[7] As far as I can tell so far, Aedes species don't make use of the drop for cooling. Male mosquitoes don't heat up because they don't feed on blood so they rely on environmental temperatures for heating and cooling.[7]

So much more reading to be done (apologies for errors above - I'm still learning about mozzies) - just not of data from Brazil.

References...
  1. Thermal Stress and Thermoregulation During Feeding in Mosquitoes
  2. https://en.wikipedia.org/wiki/Insect_thermoregulation
  3. http://www.vanderbilt.edu/hillyerlab/Research__Circulation.html
  4. http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0002190
  5. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961054/
  6. http://www.ncbi.nlm.nih.gov/pubmed/18021028
  7. http://www.cell.com/current-biology/pdf/S0960-9822(11)01311-X.pdf
  8. https://en.wikipedia.org/wiki/Hemolymph
  9. https://projects.ncsu.edu/cals/course/ent425/tutorial/circulatory.html
  10. http://portalsaude.saude.gov.br/index.php/o-ministerio/principal/leia-mais-o-ministerio/197-secretaria-svs/20799-microcefalia
  11. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/Forms/public.aspx
  12. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961054/pdf/ehi-10-2016-119.pdf
  13. http://journals.plos.org/plosntds/article/asset?id=10.1371%2Fjournal.pntd.0002190.PDF
  14. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961054/pdf/ehi-10-2016-119.pdf

Sunday, 14 August 2016

Social media scientists - we're probably still talking mostly to ourselves...

The following is an opinion piece so it has words like "seem" and many feels. Please take it as such.

A definition of grey literature from
 The University of Queensland.[2]
The grey (US: gray) literature is that written material which is not part of the "traditional" publishing model - unpublished, privately published or non-commercial writings.[1,2,10] GreyLit can also includes blogs and tweets and other such social media (SoMe) output.

Blogs, tweets, facebook posts can all be produced far more rapidly than any peer-reviewed literature - I tweeted yesterday about having an accepted manuscript sitting with a publisher for over 19 weeks and counting. 

GreyLit can be edited easily and can reach further because it is openly accessible to the public. SoMe is a great way to distribute current events - like detail on disease outbreaks for example. But the GreyLit may not be secured by a permanent object identifier, or a stable website address, nor is it listed on the US National Library of Medicine's PubMed literature database, and its meaning can be changed when edited leaving nary a trace of what came before - these changes are often seen with public health GreyLit. GreyLit can be short-lived and may be considered risky to cite; it's volatile.

Scientists cite serious scientists...

Given all that, it's pretty unsurprising that grey writings are often uncited by the more permanent traditional academic literature (books and journal articles for example) - at least not by those in my research fields. In general, scientists stick with citing the traditional serious academic [13] scientific literature. This is despite GreyLit harbouring more timely and leading-edge discussions and often being more digestible by both the public and those scientists who are sick to death of intentionally and arrogantly dense writing.

It's pretty clear that we scientists write scientific literature for other scientists-it's a great place to catalogue full descriptions of methods and expert evaluation.[3] 

Of course, even serious science does not always get cited by other scientists.[3] It's difficult to gauge how much it even gets read. It can also sit behind a "paywall" - a closed access approach requiring payment to cover article production costs and to make a profit for the publisher - it is a business not a charity. To get a scientific publication into an open access platform, an author's grant or institution pays for the privilege. Costs vary (nicely outlined in this piece from 2013;[4]).

Papers keep coming out at an increasing rate...


Biomedical publications listed on PubMed
Made by searching on date +/-
journal name.
Click on image to enlarge.
Biomedical publication numbers are increasing each year according to PubMed numbers (see the graph).

In 1992 there were a third (416,310) as many publications on PubMed as there were in 2015 (1,244,277). In 2004 half as many as in 2015. Conventional paper printed (+ online) journals do not seem to have scaled their output to keep pace with this rate of increase - so it may follow that many top tier papers have to find homes among less luxurious journals. Purely online journals, like PLoSOne in the graphed example, do seem to scale with demand-being online makes them more nimble and accommodating. A win for them and a plus for science, researchers and the public if that journal has a reliable and trusted brand. 

What about the many, many new fee-for-publication "journals" appearing? There is no evidence that many of them are trustworthy at all. Some have yet to be around long enough to get listed on PubMed and there is a justifiable sense that in publishing with them, ones work may never get editorial support or be visible to search in the future. Another risk - this one to science in general - is that some of these journals have been clearly identified as predatory (in it for the $$$[11,12]). 

Predatory journals may simply be a dumping ground for badly written bad science that is poorly or not reviewed and a wasteland for science that is not visible to standard search methods. And it may be volatile. A new type of GreyLit. 

While it may be a great feeling to add papers to the publication list of a curriculum vitae (CV), it will ultimately reflect poorly on scientists because poor science and conclusions will be ignored or be challenged and found wanting. None of this is good for the science brand.

But what about academics talking to the public directly?


When we unserious academics venture onto SoMe to be unserious, we may still be talking to ourselves. We tend to attract followers who are like-minded and/or have a mindset that already leans towards the search for knowledge and understanding. Such followers seem like people who generally read a lot, they are willing to learn new things and they don't usually just accept what they read in their timelines to be the absolute truth. I love discussing stuff with them - it can get robust at times -but that just challenges us all and that is a good thing. I just don't think these followers necessarily represent the majority of our communities. 

How can we scientists drop reason into the mix of conflict, rage and ignorance that is seeking to darken the lives of communities everywhere? 

Perhaps by more of us stepping up. 

Some of my peers are thoroughly knotted up in self-indulgent arguments around only speaking in public on research topics they are expert in. This parochial and short-term view is at odds with the likely benefit that years of experience in logical and ordered thinking and problem solving could provide to the chaotic world our communities are increasingly faced with. 

But academics adding to the GreyLit are faced by the real need to spend our writing time predominantly on scientific journal articles and grant applications. The GreyLit may still not be seen to add value to a CV that is needed in order to get/keep a job and pay the bills-even if a single good piece may reach tens of thousands of people, instead of ten.

Today we can seek out the facts we want to read...

The public can now individually collect and curate their own sources of news and information much more easily than we used to; they can feed their existing biases.

Not that long ago we relied more on a limited range of radio, TV news or newspapers to find out what was happening in our local or global communities. We had that material delivered by professional journalists (yes, there were exceptions). But now we can source our news ourselves or from like-minded anonymous avatars who gather together news snippets into what they consider a theme, may do no research or have any understanding of the history underlying a topic, have no grasp of the subject or of when balance is or is not needed and feel no need to present information with accuracy. Kinda like those real journalists used to do. But today's "journalism" - a seemingly shrinking profession anyway - often seems relegated to the production of suitably emotive and inflammatory clickbait. The new news curators run on feels and likes and their followers are thus "informed". 

You have to look no further than recent events in the UK and US to see examples of how this can have real world outcomes.

The age of expertise is gone, welcome to the age of extreme emotion... 

Those of us academics who wish to continue being unserious but who wish to help provide factual information in an age of anti-expertise [5,6] and anti-intellectualism [7,8,9] are faced with some real challenges. 

How do we make sure all our lab/bench/desk work is not wasted effort and dollars? 

How do we help turn around some of the dangerous, illogical and factless sentiments polluting our peace? 

How do we join in new discussions we may not be expert in but feel we can contribute to, without getting called out or piled on?

If few are reading science and the public are not understanding science and if science is not contributing to the daily discussion and if the loudest most emotive voices are the ones that determine our future, then politicians will not be driven to fund science and teachers will not be empowered to teach science and logic, and science will increasingly stop being done. 

That outcome is just not acceptable. 

So the main question I leave you with is, how do we unserious scientists reach the audiences we'd like to write for - those who are not simulacra of ourselves? 

References...
  1. https://www.une.edu.au/library/support/eskills-plus/research-skills/grey-literature
  2. http://guides.library.uq.edu.au/how-to-find/grey-literature
  3. http://blogs.lse.ac.uk/impactofsocialsciences/2014/04/23/academic-papers-citation-rates-remler/
  4. http://www.nature.com/news/open-access-the-true-cost-of-science-publishing-1.12676
  5. https://www.theguardian.com/tv-and-radio/2016/jul/02/professor-brian-cox-interview-forces-of-nature
  6. http://www.theguardian.com/politics/blog/2016/jun/08/experts-eu-referendum-michael-gove
  7. http://www.huffingtonpost.com/bill-e-white/america-dumb-and-dumber_b_5670293.html
  8. https://www.psychologytoday.com/blog/wired-success/201407/anti-intellectualism-and-the-dumbing-down-america
  9. http://www.smh.com.au/small-business/managing/work-in-progress/we-love-being-dumb-and-dumber-20150108-3nraf.html
  10. http://www.greylit.org/
  11. https://en.wikipedia.org/wiki/Predatory_open_access_publishing
  12. https://scholarlyoa.com/2015/01/02/bealls-list-of-predatory-publishers-2015/
  13. https://www.theguardian.com/higher-education-network/2016/aug/05/im-a-serious-academic-not-a-professional-instagrammer

Wednesday, 3 August 2016

Spillover: tales of the zoonosis...

I highly recommend this document on tonight in the United States and hopefully coming to your country soon thereafter.


I had a small advisory role (see proof below!) on this over the course of about 19 months and I can assure you that it is a beautifully put together, visually delicious and educational summary of some of our planet's most recent animal>>human viral outbreak events.


Spillover credits, Page 1.