Saturday, 2 September 2017

VDU has moved house....

If you're looking for new posts about viruses and virus-related stuff (which coudl be anything really!), from now on please go over to the new site with its easy-to-remember address...

virologydownunder.com

Hope to see you there!

Cheers,
-Ian

Wednesday, 16 August 2017

This little MERS-CoV infected piggy had RNA, but that little piggy with indirect contact had none...


Back in April, a Spanish/Dutch collaborative study came out looking at whether pigs deliberately infected with Middle East respiratory syndrome coronavirus (MERS-CoV) might be able to transmit that virus to other pigs.[1] Turns out they can, but so weakly that the authors concluded pigs are unlikely to be a source of virus in the wild.

Alpacas have been use for transmission studies in the past - these furry four legs do seem to be able to host and transmit MERS-CoV once infected, and in the wild, and may have a role in keeping the virus alive among animals. They may also be a source for spillover into humans on occasion; check out MERS-CoV: alpacapalooza for a reminder.[2]

But what did this new study do?

First up they infected a  group of 5 pigs (P1, P2, P3, P4, P5) with a fair whack (107 TCID50 (50% tissue culture infectious doses) of the HCoV-EMC/2012 MERS-CoV virus variant by shooting 1.5ml of virus in saline up each nostril of the pig's noses. None of the pigs showed any measurable signs of illness - no temperature rise or respiratory signs. That result alone shows that otherwise healthy walking bacon is not a model of  MERS (the disease).

After 2 days, 5 uninfected pigs were added to the same cage to permit direct contact (touching snouts and other stuff that pigs do to each other when in the same space); P6-P10. This group were called 'direct contacts'. They represents your Mum & Dad - the ones who keep kissing you while you're in hospital with MERS (not that kids often get sick with MERS-CoV!).

A third group of piggies were housed in a separate pen, 30cm away, and called 'indirect contacts'. They represent that cousin who came to visit you in the hospital, but just sat in the corner playing PokemonGo on their tablet because they didn't really like you anyway but got dragged along by your Uncle.

A lot of different samples were taken from the pigs from before inoculation and at various intervals up until 26 days afterwards. The results from testing these samples break down as follows:

  1. Cell culture studies found that only the MERS-CoV inoculated pigs shed infectious virus and developed an antibody response to MERS-CoV spike protein (measured by S1 ELISA) or that were capable of neutralizing MERS-CoV in cell culture experiments.
    Neither of the 2 contact groups shed detectable infectious virus or mounted an immune response. 
  2. Sensitive molecular methods (RT-PCR [3]) found that the inoculated pigs all shed MERS-CoV RNA from day 1 after inoculation; 3 stopped shedding after day 7. 3 of 5 direct contact pigs shed MERS-CoV RNA between day 3 and day 5. These pigs entered the infected pig's pen at day 2-were they being infected by residual inoculum?
    A sample of virus left on the bench for a week and a portion tested each day in cell culture and by RT-PCR would have been useful to assure us that infectious virus from the original inoculum wasn't the only thing being detected in this study
  3. Some viral RNA was detected in air samples collected between the two pens and from some wall/surface swabs - but infrequent and in very small amounts
So, the study concluded that infected pigs may transmit MERS-CoV but that if they do, it's a pretty inefficient process. 

It's not clear to me whether the initial P1-P5 were successfully infected by MERS-CoV at all. The piggies had virus given to them, sure. But did that virus enter cells and replicate within those cells to assemble new viruses? If it did, were those new viruses infectious? Did new viruses release from the infected cells and infect new cells and the other pigs, or was this all detection of eh original inoculating virus? 

The immune responses detected only in the inoculated pigs may have been the response to inoculum, without MERS-CoV replication. The very small amounts of viral RNA detected in indirect contacts and in the air and on some surfaces could also be leftover inoculum spread from the noses of P1-P5. Without knowing how long MERS-CoV in saline remain infectious or detectable under their conditions, we cannot answer that. We do know that MERS-CoV can remain infectious for 2 days and be detected by RT-PCR methods for at least 5 days.[4,5] 

So all in all, the main contribution of this study to the furthering of MERS knowledge is its ability to rule out pigs as a useful animal model for disease or transmission.

References...
  1. Middle East respiratory syndrome coronavirus experimental transmission using a pig model
    https://www.ncbi.nlm.nih.gov/pubmed/28653496
  2. MERS-CoV: alpacapalooza
    http://virologydownunder.blogspot.com.au/2016/09/mers-cov-alpacapalooza.html
  3. Reverse transcription polymerase chain reaction (RT-PCR)...a primer
    http://virologydownunder.blogspot.com.au/2015/05/reverse-transcription-polymerase-chain.html
  4. Middle East respiratory syndrome coronavirus: how tough is it?
    http://virologydownunder.blogspot.com.au/2013/10/middle-east-respiratory-syndrome.html
  5. Korea contamination: Middle East respiratory syndrome coronavirus in the room..
    http://virologydownunder.blogspot.com.au/2016/09/korea-contamination-middle-east.html

Saturday, 15 July 2017

900 words on some general stuff about viruses and those other bugs...


We (Dr @kat_arden and I) were invited to contribute one part to a four-part series in The Conversation this week - and after a lot of no...yes/no/yes from yours truly (I do that a lot these days), we put this piece together.

If I was still a researcher this might be classified 'public service' - but as a simple scientist these days, it's simply science communication. 😀

Now. Back to trying to get back into blogging about viruses. Or writing the MERS review. Or writing up my own old data... 😱

Sunday, 9 July 2017

Ebola virus disease over in the DRC....

Another year, another outbreak of Ebola virus disease (EVD) overcome in the Democratic Republic of the Congo with the help of a mix of expert local skill and knowledge, isolation and rapid global response.

The World Health Organization have summed up the end of an outbreak in which 4 died, 5 cases were lab confirmed and there were a total of 8 likely EVD cases.


References...

  1. http://www.afro.who.int/en/media-centre/pressreleases/item/9744-who-declares-an-end-to-the-ebola-outbreak-in-the-democratic-republic-of-the-congo.html

Sunday, 2 July 2017

Editor's Note #27: Anakin Fencewalker joins the Force...

After 19 years, our furry family member had to leave us this Wednesday. His quality of life was decreasing and he had stopped eating - he made the call and he let us know.

He is missed enormously and remembered daily by his human family, for many things.

He saw two PhDs completed; he sat through the writing of 70+ papers, a book, 14 chapters, 11 reviews (all had late night writing components that required pats and scratches), he watched over the growth of two babies and has been with them all their lives; he lived in the two houses my family have known; he was a constant companion to my wife and he kept me (and my keyboard) company while I wrote many pieces for this blog.

Anakin Fencewalker.
12SEPT1998-28JUL2017
Thankyou Anakin.

May the Fence be with you.

Saturday, 24 June 2017

Another canary in the same coalmine - mild MERS may be bad news...

Sometimes, the Middle East respiratory syndrome coronavirus (MERS-CoV) is detected in a person who is not ill. 

Weird huh? 

Not really. This is the result of laboratory testing of contacts of a known and infected person during the process of containing a potential outbreak.


For me personally, this is one big question about new or emerging viral infections or infections we are still learning about - like new influenza viruses, MERS-CoV, ebolaviruses and Zika virus. Do we really know how often a laboratory-confirmed infected person with mild or no illness can spread virus to a new person - an uninfected potential host? Are our tools up to the job of detecting what's happening and are we using them properly?

Conventional wisdom is that truly asymptomatic but virus infected people do not infect others around them, or if they do, it's a pretty rare event. Because the risk is seen as low, studies around this issue are often down the list of research priorities.

The importance of this issue lies in whether mild or asymptomatic people need to be more closely considered as having a role in spreading virus and contributing to community or hospital outbreaks.

Emerging from the 2015 South Korean MERS-CoV outbreak, a recent report described the findings from laboratory testing of 82 contacts of an asymptomatic healthcare worker.[1] No other person became MERS-CoV positive. I have some issues with the fact that the nurse herself does not seem to have been tested to show that she developed antibodies to MERS-CoV and there also isn't a lot of discussion about how the PCR testing for MERS-CoV can be a bit "flaky" when sampling once from the upper respiratory tract. Although, there aren't any sampling details in this paper either (I'll blog about this paper another day)!

But I digress. 

I've plotted the all the publicly available mentions of asymptomatic MERS-CoV infections, by week, in the graph below (the bottom panel). 

Click on image to enlarge.
The yellow peaks show that cases without illness usually correlate with healthcare workers in the graph above, during hospital and healthcare facility outbreaks (see my previous post describing the pink graph in the top panel).[2] 

This isn't too surprising. The majority of disease associated with MERS-CoV infection arises in older males who already have an underlying disease including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions. Healthcare workers however are usually younger and do not have, or have not yet developed, such comorbidities. 

MERS-CoV is often a shown to be a bit of a bully when challenged by a healthy younger host's immune system. Although, when hit with a larger primary dose of virus from an infected camel, even the healthy can get hit very hard.

Healthcare workers can be the 'canary in the coalmine', except singing about a healthcare outbreak rather than a gas leak. Similarly, laboratory confirmed MERS-CoV infection manifesting with only mild or no signs and symptoms of disease, also serve this role as a sentinel of hospital, rather than camel-to-human, transmission of MERS-CoV.

References...

Tuesday, 20 June 2017

Working for health can make you sick....

Below is a quick look at the percentage of total Middle East respiratory syndrome coronavirus (MERS-CoV) cases reported each week that are listed as being healthcare workers (HCWs).



The sources of the numbers used in this graph.

These data are curated by me for this blog in my spare time and are compiled from the Kingdom of Saudi Arabia'a Ministry of Health (MOH) daily reports, the World Health Organization (WHO) disease outbreak notifications (and relatively new line lists) and from the FluTrackers line list

I use the same numbering as FluTrackers use in an attempt to produce at least two lists that agree on numbering and content. 

Some other things to note about this graph..

Each of the pink "spikes" is a percentage calculated by dividing the number of MERS-CoV laboratory confirmed HCW by ALL of the MERS-CoV laboratory-confirmed cases that were reported in that same week... 
Sometimes there might be just 1 HCW and 1 patient - which would give a pretty big looking 50% positive (1 divided by 2). But clearly, it is just 1 HCW. 

So proportion (%) alone is not a whole lot of use sometimes. One needs to know the denominator (the bottom number of a fraction) to get a gauge of how big the problem really is. 

The current June hospital outbreak in Saudi Arabia includes three facilities in Saudi Arabia according to the WHO and the MOH.[1,2] From the 47-year old male reported on the 1st June as an index case in one facility, there have been about 44 secondary MERS-CoV detections (cases) in Riyadh. 

Of the 44 MERS cases, 26 are listed as HCWs; 18 of 25 HCW MERS cases occurring in a single week (week beginning 5th June) and accounting for the 72% spike seen at the end of the graph above. 

Just to confuse things, there were 3 distinct hospital outbreaks that occurred previously,  in April and May, but it's not clear whether they contribute any cases to the June tally.[3]

Why can't we have nice things?

There has been no other successful effort, by anyone, to produce a single public MERS case list with a universally agreed upon numbering scheme that contains useful but deidentified case detail, that everyone could refer to and use. The same applies to the influenza A (H7N9) virus as well. This has only been achieved by public volunteer bloggers; FluTrackers and this blog. Pretty poor when you think on it.

References...

  1. http://www.cidrap.umn.edu/news-perspective/2017/06/who-details-saudi-mers-clusters-outbreak-grows
  2. http://www.who.int/csr/don/13-june-2017-mers-saudi-arabia/en/
  3. http://www.cidrap.umn.edu/news-perspective/2017/06/who-reports-3-saudi-hospital-mers-clusters-new-cases-uae-qatar

Sunday, 18 June 2017

Climate and science denial....

I'm in a reading and watching phase at the moment - not much time for writing. Two videos I've recently come across are so good that I've embedded them below; they are just so good at describing their topics.

Yes, I know this is not directly abort virology - but climate change (CC) and science denial very much does indirectly impact on the fields of virology - some example include

  • virus transmission
  • imported infection disease
  • mass gatherings and disease
  • virus vaccines
  • viral immnuology
  • emerging virus diseases
  • viral zoonoses
  • seasonal viruses


These two vids are also just important science communication tools for all of our everyday lives. Show your kids. So I've bookmarked them as much for my own future reference as for yours.

1. Why reducing carbon emissions matters. 

This was lifted from an article at The Conversation.[1]


  

2. Denial 101x: five characteristics of science denial.

This was also lifted from a longer article in The Conversation.[2]



References...

  1. https://theconversation.com/the-three-minute-story-of-800-000-years-of-climate-change-with-a-sting-in-the-tail-73368?utm_source=twitter&utm_medium=twitterbutton
  2. https://theconversation.com/one-nations-malcolm-roberts-is-in-denial-about-the-facts-of-climate-change-63581

Sunday, 21 May 2017

Ebola in the DRC: list of border-checking countries at seven...

Starting from WHO Regional Office for Africa Ebola Virus Disease (EVD) Situation Report No. 2,[1] there have been an increasing number of countries that are screening ill-looking people for EVD at their ports of entry. Currently [7] there are 7 and they are:

  • Kenya
  • Nigeria
  • Rwanda
  • South Africa
  • United Republic of Tanzania
  • Zambia
  • Zimbabwe 

Quite a few more than I listed yesterday. 

Latest EVD figures form the DRC.
Click on image to enlarge.
No borders are closed to travellers from, or who have travelled through, the Democratic Republic of the Congo, which is good news.

Screenshot from SitRep No.5.[1]
Click on image to enlarge.
Presumably this screening relies on the appearance of signs of illness, questionnaires and perhaps thermal camera images to identify feverish people.

As I alluded to yesterday, these efforts are not very effective at actually picking up EVD cases from among a milieu of other febrile illness that stumble through a port of entry.

Studies - some of which are summed up in this Canadian review [2] - are usually not supportive of any practical benefit from using fever as a screening tool to pick out a single disease in passing travellers.[3,4,5] 

However, these screening efforts do play a role in making citizens and politicians feel better and more useful. The precautions may also be helpful in keeping travel flowing.[6] Whether the continued flow of travel during an epidemic that may leak from a hotzone is a good thing or not will no doubt (once again) be dissected after a more more transmissible pathogen sweeps across the world I expect.

References....

  1. http://apps.who.int/iris/bitstream/10665/255463/1/EbolaDRC-1652017-eng.pdf?ua=1
  2. https://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0071254/
  3. http://afludiary.blogspot.com.au/2011/05/study-thermal-scanners-pandemic.html
  4. http://afludiary.blogspot.com.au/2014/11/eid-journal-evaluating-border-entry.html
  5. http://afludiary.blogspot.com.au/2014/10/why-airport-screening-cant-stop-mers.html
  6. https://www.ncbi.nlm.nih.gov/pubmed/27390092
  7. http://www.afro.who.int/index.php?option=com_docman&task=doc_download&gid=10836&Itemid=2593

Saturday, 20 May 2017

Ebola virus disease in the DRC: first graphs...

The World Health Organization have apparently found an outlet for their Ebola virus disease (EVD) reports for 2017's Democratic Republic of the Congo outbreak.

It's not the Disease Outbreak News site. It's not the WHO media page. It's not any of the past EVD outbreak pages on the central WHO site.

Turns out the Situation Reports (SitReps) are to be found on a new page on the WHO African site.[1] Okay. Why not? Found it eventually. I've plotted the first 4 (they started from 15th of May) below. Not much to say about trends at this early stage obviously!

Click on image to enlarge.
Don't go expecting to find how we got to the totals shown on the 15th - those may well be lost details. Or they may come out later. We'll have to wait and see. Outbreaks viewed from the public point of view are very much about patience and trying not to leap to any dramatic conclusions - like those decisions taken by at least one country in Africa to start screening passengers for signs of EVD.[2] It's your budget guys - spend up if it makes you feel safe. At this stage, and perhaps ever, its a pretty wasteful exercise though; apart from your citizens seeing you doing something.

Back to numbers. I'm pretty impressed with the WHOAfro SitRep - the 4th Report carries a detailed table of cases, deaths and locations and also a timeline graphic (below) which is fantastic. 

Click on image to enlarge.This image is part of SitRep No.4.[3]
And to wrap up, just for a glimpse of what has come before and where we are now (and because I promised @kristindownie I would!), I've also added an updated "EVD through time" bar graph. Where we are with the current outbreak total is highlighted using a red arrow and the towering totals of West Africa are indicated by yellow arrows.

Click on image to enlarge.


References...

  1. http://www.afro.who.int/en/ebola/ebola-situation-reports.html
  2. http://www.premiumtimesng.com/news/231328-ebola-nigeria-intensifies-screening-at-airports.html
  3. http://apps.who.int/iris/bitstream/10665/255526/1/EbolaDRC-1852017-eng.pdf?ua=1

Saturday, 13 May 2017

Ebola returns to the Democratic Republic of the Congo (DRC): Zaire...

UPDATE No.1 14MAY2017 AEST
UPDATE No.2 15MAY2017 AEST
UPDATE No.3 17MAY2017 AEST
UPDATE No.4 18MAY2017 AEST
 UPDATE No.5 18MAY2017 AEST
The World Heath Organization alerted the world on May 12th [1] to an outbreak of Ebola virus disease (EVD) in Likati, a remote region in the Bas-Uele province of the Democratic Republic of the Congo (DRC).[4] The news had been communicated to them on the 11th May by the DRC Ministry of Heath.[6]

This is the 8th recorded outbreak in the DRC and it is hoped that their expertise, together with a range of rapidly mobilised outside expertise, will contain this one quickly and with a minimal loss of life.[5]

It reportedly took 10 days for the first samples to reach the lab in Kinshasa for testing.[8] Google estimates about 47 hours  to travel the ~3,000km from Kinshasa to Aketi (about 50km beyond Likati via Google's inland suggested route - doesn't account for off the 'main' road and forest parts) - it doesn't give estimates for Likati direct. The WHO explained...

See thread here if you use Twitter.
The journey to Likati is not an easy one.[16] Planes and helicopters are being used and there are questions around how secure the area is.[18] While remoteness is anecdotally beneficial for containing the spread of an outbreak, there are 2 clusters of illness and death outside of Bas-Uele, marked on the Ebola SitRep maps, which may test this theory.[17]

There are reportedly 300,000 (GAVI/Merck emergency stockpile [13])-700,000 doses of the  rVSV-ZEBOV vaccine which has been reported to be highly effective at preventing EVD.[3,9,10]

Early numbers were a bit confusing [2] - as often happens in the fog of announcement of an outbreak - but since 22nd April there seem to have been:
  • 20 suspected and confirmed cases in total [17]
    • 3 fatal cases (proportion of fatal cases: 15%)
    • 1 of 5 samples was initially laboratory confirmed (PCR) at Institut National de Recherche Biomédicale (INRB) in Kinshasa - it tested positive for Zaire ebolavirus
    • a 2nd case has since been Zaire ebolavirus lab confirmed [12]; 3 have tested negative [17]
    • at least 6 cases hospitalised [7]
    • ≧416 contacts being traced [17]
    • 1st case - 45 year old (or 39yo) male (45M) transported by taxi; died on arrival [11]
      • driver fell ill and died
      • carer of 45M fell ill and died (=25 contacts) 
    • Nambwa health district has notified the greatest number of the earliest cases: 13 in all, with 2 deaths (case fatality: 15%).[15]
 

References...

  1. https://twitter.com/WHO/status/863022054223773697 
  2. https://www.theatlantic.com/science/archive/2017/05/a-new-ebola-outbreak-in-the-democratic-republic-of-congo/526506/ 
  3. http://www.npr.org/sections/thetwo-way/2017/05/12/528124232/ebola-death-confirmed-in-democratic-republic-of-congo 
  4. https://www.wired.com/2017/05/ebola-returns-central-africas-virus-hunters-ready/ 
  5. https://foreignpolicy.com/2017/05/12/ebola-returns-in-congo-a-test-of-next-time/ 
  6. www.minisanterdc.cd 
  7. http://www.who.int/csr/don/13-may-2017-ebola-drc/en/ 
  8. http://www.mysanantonio.com/news/local/article/New-Ebola-case-reported-in-Democratic-Republic-of-11143890.php?cmpid=twitter-tablet 
  9. http://www.sciencemag.org/news/2017/05/will-vaccine-help-curb-new-ebola-outbreak-drc 
  10. http://www.nature.com/news/ebola-vaccine-could-get-first-real-world-test-in-emerging-outbreak-1.21989 
  11. http://www.afro.who.int/en/media-centre/pressreleases/item/9609-dr-moeti-in-kinshasa-to-discuss-reponse-to-ebola-outbreak.html 
  12. http://www.reuters.com/article/us-health-ebola-congo-idUSKCN18A0ZP
  13. https://www.newscientist.com/article/2131131-ebola-once-again-on-the-prowl-as-emergency-teams-stand-ready/
  14.  http://reliefweb.int/report/democratic-republic-congo/ebola-virus-disease-democratic-republic-congo-external-situation-0
  15. http://www.afro.who.int/en/media-centre/pressreleases/item/9631-drc-response-to-the-ebola-virus-disease-outbreak-in-bas-uele.html
  16. http://www.radiookapi.net/2017/05/15/actualite/sante/ebola-en-rdc-defis-et-chances-dun-lointain-enclavement 
  17. http://apps.who.int/iris/bitstream/10665/255486/1/EbolaDRC-1752017-eng.pdf?ua=1 
  18. http://www.healio.com/infectious-disease/emerging-diseases/news/online/%7Bf835f3ce-da12-4ae7-9c8c-0e0f3d6ef8f3%7D/extent-of-ebola-outbreak-in-drc-may-not-be-known-for-weeks

Maps used to help place Likati and Bas-Uele...
      Updates...
      1. Fixed spelling mistakes in Likati, added detail about sampling delays
      2. Added references 10-12; noted 2 cases now confirmed, 19 suspect cases in total 
      3. Update on where the 300,000 vaccines come from [13]
      4. Update on contacts and ReliefWeb and WHO references
      5. New SitRep from WHOAfro - altered case & testing numbers

      Sunday, 16 April 2017

      March...for Science...this Saturday 22nd April...

      Hi All,


      Reprinted with permission from
      I hope you can make some time this coming Saturday 22nd April to get to your local March for Science venue, wave a sign and listen to some talks. 

      Check out the Australian website for details https://marchforscienceaustralia.org/ and RSVP to help the organisers understand how many will be attending.

      It would be great to see as many scientists and members of the science-supporting public turn up to support the ongoing need for science in our everyday lives. 

      As the local Australian supporters page details, the March for Science aims to celebrate that scientific knowledge delivers...
      • community knowledge and understanding about the world(s) around us
      • information about new disocveries that is clearly communicated for eveyone to understand
      • facts to underpin public policies that guide our way of life
      • results that are deserving of ongoing long-term funding

      I'm not involved in the march organisation but I hope to be at my local Brisbane march - along with my science loving family. 

      After cleaning our teeth with toothpaste and fluoridated water - both of which have scientific data to prove their effectiveness - we'll probably drive there in a car fabricated, assembled, painted, tested, fuelled and imbued with safety devices that have all resulted from scientific advances. 

      We'll drive to the city on roads and bridges designed and made thanks to scientific achievements. We'll be singing along to the Moana soundtrack - a digital download copied onto a CD  from a movie we saw - every step of which was made possible thanks to a slew of scientific innovations and with storytelling bolstered by scientifically accurate research. 

      We'll be wearing clothes made possible by scientific advances in fabric design, machining and colouring, assembled by people using machines that were produced from numerous individual scientific breakthroughs. We'll have applied sunscreen of a formulation that has been proven to reduce skin burning while we stand in Queensland's high ultraviolet midday sun. Sunburn has been shown through medical research (science!) to increase the risk of developing skin cancer later in life. One of my son's will be actively and safely mounting an immune response to his recent HPV vaccine - a development that will reduce his risk of some cancers, and reduce the risk of him passing along the virus that may cause such cancer in others.

      I'll also be wearing a machined cap to protect my head from burning. It will be embroidered with a computer-designed rhinovirus logo. Thank goodness for a vast array of scientific advances that that lead to computers, communication networks, financial transaction systems, broadband cabling and the internet via which I write this very blog (while consuming too much chocolate - which medical science tells me is overly laden with sugar and fat so as to be bad for me if I consume it regularly while continually sitting on this chair).

      There's a good chance I'll have taken some pain relief for a headache caused by a (probably rhino-)virus-induced common cold. The drug and the knowledge of the virus were all generated by medical doctors, chemists, physiologists, virologists, epidemiologists and other researchers generating and using science in a whole range of ways over decades.

      Later we'll grab some lunch from a vendor that has made and stored the food in ways that mean we won't end up with food poisoning later (we hope) - because of lessons learned about microbes and food storage through the application of the scientific method and ongoing scientific checks. 

      And that's just a sampling of the science that will permeate our lives during this one day.

      Science is everywhere and we are wholly dependant upon it in our big city and suburban lifestyles. Science makes us safe. It allows us to work and to travel and to communicate (reading this on a mobile device much?) more effectively. 

      Science permeates our life in ways we already know and in ways we have yet to understand. Imagine what continuing the support for science will lead to in the near and distant future.

      We will March for Science because science has mostly made our lives better. 

      Monday, 27 March 2017

      Happy 4th birthday...

      This blog!

      I'm sure somene one said that a year in social media equates to 7 cat years. Maybe it 9.


      Anyhoo, I'll be hunting down a cake for us all today - or maybe a muffin at the canteen.

      My heartfelt thanks to those who have made writing for this blog so much fun. 

      I hope we all keep learning about viruses together. Anything is worthwhile if you learn something from it. ...and have a reference to prove it was based on data...and cite that reference...and it gets cited by others...and peer reviewed....

      Happy 4th!!


      Sunday, 26 March 2017

      The week that called out to me....

      Me.

      It’s been an interesting week in which some stuff was said about what I believe, how I unjustly unfollow people, how I see myself and how terrible I am to students. If you didn’t see any of what this refers to but are interested – see the Storify here.

      This started when I suggested anyone could come together for the March for Science. I disagreed with some who said before we can march alongside each other in a common cause to value fact over fake, science should be perfectly balanced and inclusive. 

      It was surreal to read how that spun up such specifically disparaging commentary delivered by people who didn’t know me at all. They hadn’t never gone to school or university with me, worked in science with me or been a student of mine. They had never even met me face to face. But they felt they had me all sorted out. Digest that for a minute; existence defined entirely by your last series of 140-character word exchanges in a darkened room full of shouting people? What if you hadn’t even said the things you were accused of saying? What if others who knew you better were silent? Friends are those who stick around.

      Some insightful conclusions included that I was an absolute troll, a bigot, atrociously behaved, uncaring, incapable of basic kindness, horribly offensive, executing ad hominem attacks, a dick, noisy, abusive, a member of the tone police, a whitesplainer, a lost cause, a denier of realities, someone who doesn’t listen, argumentative (totally agree with that one), fragile, defensive (am not), a liar, sarcastic (okay, I added the one), someone who paints people in a bad light with no chance of response, a hole digger, biased, an ultimate betrayer, a victimizer, someone who punches down, a disappointment, tone-deaf, a clueless white man, march for science sentinel on troll patrol, well-meaning but unable to see past my privilege, someone who flees, gross, a seeker of validation, snide, generally deaf, a mis-stepper, a poor judge, not a good guy, intransigent, having my head up my own ass, wrong, reprehensible, a white male (yep), dismissive (I agree, I don’t stop to acknowledge other’s points often enough) and someone who doubles down.  

      Not one mention of curmudgeon? 

      Isn’t it impressive how people can be so accurate and specific in summing up someone, just through a few tweets? 

      I’m writing this post for me (lots of “I” and repetition) and perhaps just to note that I have listened to what many have been saying for years now. I expect this text will be sampled and held up as an example for fragile white male privilege, support for …everything bad… and that I’m the only person still talking about this. If gas-lighting is about getting someone to question their own sanity, many people, including a couple I really had thought better of, did a wondrously expert job at making me doubt my own mind over the past few days and this is my final part of working through all that.

      I’m aware of my ignorance on diversity, but don’t let facts stand in your way.

      If someone wants to read between the lines of the next few points – perhaps their conclusions will say more about them than me. 

      I have zero illusions about my absence of expertise on and around the topics of diversity, URM, POC, WOC, LGBTQI, MfS, PWD, intersectionality or #marginsci (look them up - I had to). Not once have I portrayed myself as an expert in these fields. If someone has wasted keystrokes telling me I don’t know what I’m talking about, it might have been because I don’t. I leave that to experts like Dr. Zuleyka Zevallos (@OtherSociology).

      We don’t need facts to make authoritative sounding claims and statements. Today the United States presents itself to the world through a fog of “alternative facts” and “fake news”. Other countries, including Australia are also guilty of this. Science should be better than that. I believe it is better than that. But there are exemplars within science, as there are within any human group, of racism, sexism, colonialism, marginalisation and misogyny. There are bullies wandering around looking to call people out (see this piece on call-out culture) because bullies want to create a fight they can win and then parade the evildoer’s head around their clan as if that is an achievement. If people join in celebrating such unscientific and bestial victories, they are not living up the scientific method they purport to hold dear. 

      Across two decades I’ve been privileged to mentor a couple of dozen students. This past week saw strangers online labelled me as a “silverback in training” who “punches down” to students (more later). This was clearly based on these people having no knowledge of me in real life. They jumped to conclusions. They didn’t act like scientists but like bullies and they were flat wrong. When so-called scientists or supporters of science chose feelz instead of facts, they lost credibility. People who didn’t read the source material yet passed judgement on intent and character, should ask themselves if they support science at all, or just like to misrepresent, threaten, yell and pre-judge. I have been privileged to have a good education, home and family and I try and use that to give back in various small ways. I don’t use my privilege to bully. Do you?

      It was interesting watching the binary thinking on Twitter over the past week. Subject matter became all of that thing, or none of that thing, black or white – that thinking usually doesn’t help discourse. When I didn’t specifically spell out my position on everyone’s particular interpretation of a subject, I was deemed by some to have taken an opposing position to their beliefs and concerns. This was a teaching moment for me. I’ve often defended Twitter for being a venue where, with some care, you can convey your meaning and intent clearly.  But I was completely wrong and clearly naïve; I couldn’t even convey intent to those who I thought understood me a little. You can only communicate that level of subtlety with family and friends and with others who are willing to go back and forth; who are willing to answer questions at face value, ask questions, withhold assumption and conduct an actual discussion, with pauses to think and some space to clarify missteps. Discussion cannot happen against a gang or those pre-loaded for a fight in which they have already mentally engaged with an enemy. 

      Some diversity exists in science labs, but I do not mean to imply that science is diverse enough…

      Labs I’ve visited or worked in, those that I’ve worked with or have had people I’ve known work in – virology labs, molecular biology labs, veterinary labs and diagnostic labs in the countries listed above, do have diversity in them. How does that fit with the assertions of some that science labs are “not diverse”.

      Science is not well balanced. I say that as someone who left research because of a range of imbalances. None of them were in that earlier alphabet soup list and none I could do anything about at the time. I do work to address the imbalances related to women in science and pop culture, because I have some experience with that. Those who have presumed that I believe there is equity, happiness and bounding unicorns throughout the science I have experience with are mistaken. That isn’t said to belittle others’ experience and it isn’t meant to justify that diversity is less common than it should be. I’m just stating this at face value. Please don’t call it dismissive – I am not disagreeing with anyone about anything other than with those who say that “science labs are not diverse”. I’ve seen diversity in labs in Australia, New Zealand, The United States and in a lab in the United Arab Emirates. There was likely more diversity that I couldn’t see. I’m also not arguing that what I’ve seen may simply represent tokenism. Much of what I’ve observed doesn’t reflect the makeup of the communities around us and even if science does one day reach perfect balance, problems with inclusivity may remain. 

      So, to belabour my only point in response to those who yell loudly that there is zero diversity in science - diversity in science does exist. Only point. Just that one. Sometimes people assume everything that is not said is because it hasn’t been considered, or people presume it means support for the worst of what had been brought down on them and theirs. Those presumptions derail any chance to bring others with them. They short-circuit discussion. Maybe intersectionality is not about teaching others or raising willing newbies up to help. Maybe this is just a personal crusade for some. 

      I’ve known labs where white men were in the minority. I’m not arguing with those whose experience tells me that this is not the norm but I have worked in labs with obvious diversity. Those were good labs. But they are only a miniscule sampling. I’ve sat on sex-balanced committees - was everyone able to contribute and be heard equally? I didn’t think about inclusivity at the time. I’ve spent most of my working life directed or managed by people in some kind of minority (in my country); never directly by a woman though. But women have occupied leadership roles, above my male managers, in different organisations that I’ve worked in. I’ve been lucky to see that because the data shows that it’s not the norm, yet some progress is being made. 

      If labs exist filled only with privileged white male scientists, I’ve personally yet to see one. But labs run by these men remain very commonplace. Including human diversity in science is essential. The culture of managing humans in science roles has always felt to me like it was the last thing on anyone’s administrative tick list. Science feels like one of the holdout “old school” institutions. But today’s science is about teams and they perform best when they get along, treat each other equally, when they collaborate and when energised by the injection of fresh, new ideas and perspectives.

      I’ve certainly been privileged to work for or with some great organisations in my time in science – these have and continue to do better and to make things better by being more inclusive. They ask for help and they seek input. Overcoming institutionalised diversity and inclusivity problems won’t happen quickly – certainly not before the science march occurs. I’m also certain it won’t happen because of aggressive, overbearing, condescending groups behaving akin to privileged white men, bombarding, dismissing, overwhelming and belittling those who engage with them or disagree with their beliefs. Science certainly grows stronger from vibrant and robust discussion, but neither science nor the community will put up with bullying. Bullies have no more of a place representing diversity in science than they have excluding diversity from science.   

      “Real science labs” are diverse teams… 

      I think of a real lab as those that have a mix of the best scientists to get the job done. An idealised lab would have constructed that mix by actively biasing against the lack of diversity visible in other labs and reflecting the community it serves. A real lab works as a team with purpose, supporting and raising up its junior members using the experience and contacts of its senior ones. A real lab gives opportunities to the next generation of scientists. A real lab spends time bringing the community along with it as it explains its achievements and consciously makes itself available outside its own communication silos. 

      I never got to run a lab so I’ve never been able to control any of that. And until recently, I openly admit, I wouldn’t have given this enough attention nor would I have unpacked what that “balanced mix” meant. I’d have been navigated by what was being done around me – by the guidelines written down and by the white males running things nearby – I’m not at all proud of that. I have a wife and Twitter to thank for slowly opening me up to my lack of understanding over very recent years. In my lab roles I’ve mostly been driven by the urgency to produce papers and get grant funding and supervise new students and keep a job so I could help with having a family. This other stuff did not then have a subheading in the CV. 

      The use of Storify for its intended purpose…

      Storify is an online tool that lets us collect social media content and order it chronologically then post the list. It’s not an intuitive tool, it lacks flexibility and for tweets it means a lot of manual re-organisation if you want to try and accurately represent a lot of different, concurrent threads of conversation. I listed some of the tweets after the call-out was slowing down and kept curating it for a little while thereafter. Sure, it looks like a pedantic effort – of course it is. I also think this exchange is one others may learn from.

      To get an outside call on whether I was using the tool in contravention of any terms of service, I used the Report Abuse link to report my own Storify. Turns out that I wasn’t in breach of anything. 

      Tweets are in the public domain and all these were tweeted by adults who didn’t care how they looked or what they yelled into the world. Kinda like when you screams and gesticulates at the car in front of you because it cut you off. And then they stop and block you in and get out of the car with an angry scowl as you scramble to wind the window up. As your blood chills, you realise this is real-life and not a computer screen, and there are real consequences for your angry actions. Twitter can be an equally real yet vile cesspool of angry affectation.

      I wonder how your employer finds your behaviour online? How about your mother – or your kids when they stumble across your screen-captured swearing, probably out of context, decades from now?

      Social media 101: If it goes into the public domain, it stays in the public domain. Stand by what you said, apologise for it, or don’t say it in the first place. But don’t whine about it later; look to yourself. 

      The affront at unfollowing a person on twitter: that direct message…

      Much was made of my choice to ignore some sage advice given by another person from the twitterverse, the morning after. They suggested I apologise for all my recent wrongs and read an excellent article by Prof. Emma Johnston on how men and women can help reduce gender bias in science. It was a piece I’d tweeted and added to my Scoop.It board nine months earlier. Highly recommend it by the way - Prof. Johnston has some excellent points and an enviable writing style. 

      Some people finally read the piece and accused me of outright dismissal (Denying: one of Prof Johnston’s four Ds) of the existence of inequity. I’ve tried to explain why that is not the case here. If someone believes otherwise, please back it up with examples.

      By the time I saw the unsolicited but well intended DM I had already deleted Twitter from my phone and tablet. The @MackayIM “brand“ and everything else looked unsalvageable to me at that point. 

      When I saw the DM tweets I decided to unfollow the person to avoid more of the ‘sit down and shut up’ sage advice I’d received from people the day before. Clicking this virtual button was clearly an egregious and divisive action because it sparked a screen capture of the DM tweets by the sender which was then distributed for the next day or so. I was also blocked by this person so I initially missed all the aggrieved tweeting. 

      Just to be clear, I didn’t initially block them, just unfollowed them. Unfollowing someone on Twitter means not having to see their content in my timeline and stopping them from sending DMs to me. They could still email me of course. Or contact me on Facebook where this person had access to my profile. Or contact me though LinkedIn.

      In my opinion, DM’ing is for private one-on-one or “Direct” chats. And sure, there was no content of mine in the tweets but the intent was obvious – to malign me for the simple act of unfollowing them. Nevertheless, I get to choose who can contact me through private channels. I’m very glad I didn’t share anything personal, because it would likely have been used as further fuel for the alternative narrative fire. It’s worth remembering that Social media 101 comment above. This teaching moment reminded me that we know nothing about the integrity of the person on the other side of the screen. Just what they choose to reveal to us.

      Punching down to a junior is an unconscionable act but also a serious accusation when it’s unfounded…

      Another point on the pillory list of those who have never met me was the way I treat students. I’m told my university and employer were contacted to warn of my recent “attack” on a student I had been acquainted with on Twitter. Just to be clear, we have no student-supervisor relationship. We are on opposite sides of the planet. We had exchanged tweets since late 2014 or so, as people who have never met do. Check them out for yourself if you have real concerns. 

      The suggestion that I am acting in the role of a supervisor or mentor to any student through Twitter or that this Twitter disagreement equated to me affecting the professional life of the student or that there was any discourse between me speaking as an Advisor and anyone speaking in the role of a student is strange, perhaps ludicrous at best, and defamatory at worst. It may have affected my professional life though when a rallying call was tweeted to contact my employer (none of my online opinions are linked to any other organisation but those of the neurons in my head) because someone was offended by being unfollowed and egged others on. Unprofessional behaviour much?

      I still hear from a bunch of my past students (mostly female FWIW). My first PhD student was male. My second was a female from the Middle East. Both wrote up great PhDs. We’re still in touch. I have mentored them to the best of my abilities; I tried to teach, support and guide them well. Only they can say whether I succeeded. I am no longer a principal advisor for any student. I miss their enthusiasm and the expectation of being taught new things by them while training them in science and its lab-based politics.

      It hurts enormously to be accused of betraying the trust of a student in any way. Pain was the intent obviously, nevertheless this was a misrepresentation of an exchange between acquaintances that had nothing to do with our current career roles and was unrelated to our ages. The exchange with this person is documented in the Storify. I’m glad that I created this record despite not foreseeing this particular accusation, and despite the Storify’s creation being described as an unprofessional, biased, an inappropriate act. I’m not sure if that’s more related to how the tweeters see their own public record when they re-visit it with a cooler head, or just their frame of reference. 

      The teaching moment for me was that someone I thought knew my character a little had eagerly and publicly misrepresented that character to the world for reasons I still don’t understand. This in no way changes the fact that this person is the smartest 20-year old I’ve ever met and they would make an excellent and expert addition to any laboratory lucky enough to have them. 

      A few final thoughts.

      If I could live last week over again I‘d take back the “all” from “all labs have some diversity”. Over the past few years on Twitter I’ve been trying to remove absolutes from my vocab. Failed on that one. I also wish people had been able to pause before they tweeted their assumptions – or anger or abuse – and thought about maybe talking to me to see what I thought or believed instead of calling in and energising a thoughtless mob.   

      I’m still mulling this whole ‘call out’ fiasco over most minutes of the day, so some of these views may change, as they already have since 18th of March when this started. 

      Returning in full to Twitter doesn’t excite me right now. However, there are still 9,300 followers who haven’t yet dropped me like toxic waste. I know some of those who were quick to pick up a pitchfork are still following - they may just not have unfollowed yet. But please do - my privileged white male snowflakiness can take it and I’m unlikely to ever trust your judgement or anything you have to say. 

      When finding yourself in an avalanche like this, I recommend not defending yourself. Just stop. Right. Away. Shut up. Stop typing. Not because some loudmouth tells you to but because these are subtle conversations and the subtleties cannot be addressed in anger and never in a mob. That’s was a problem for me because I’ve spent three years aiming to respond in some way to every direct tweet I receive. The teaching moment here was that sometimes one needs to drop the social from social media. Proper discussions can be had by eMail or DM – I’ve had a few nice chats this week (thank you by the way, they each helped me a lot) – and they can be had face to face. For some without filters or empathy, it is too easy to be emboldened by the alluring anonymity of the glowing screen.  Some cannot help but say things in a way (I hope dearly) that they wouldn’t if speaking with a real person over a coffee. 

      This group was not like other groups though. They (I do not intend to be ‘othering’ anyone here, please don’t take it that way) are not like anti-vaxxers for example. I only use that example because of my recent experiences with them. The attempts by anti-vaxxers at piling on are relatively feeble, although they do share some similarities with my recent experience. Both groups tend to make ridiculous leaps in logic, to generate unsubstantiated claims and treat others with the same contempt that they rage against receiving. 

      In any social media morass such as this was, there are also sheep; desperate to be recognised but not actually contributing anything useful to the world except noise. Some members of this week’s group had much pain, much anger and some have reason and justification for it. I can imagine this comment receiving an “oh, thank you sooo much for your permission”. 

      These people are not aimless, they are not just being deconstructive and they are not selling a book or a carton of dinosaur memory water. They have real grudges for real reasons and they have a host of real issues that people like me have been integral in creating, yet only understand a bare minimum of. I was perceived to be stepping uninvited and uninitiated onto their lands.  As much as possible, I do get that. My intent was only to discuss why we as diverse human beings couldn’t support science in facing the immediate stupidity, hatred and danger at the door, and facing it together. 

      Maybe another day.

      Further reading...

      If you want to learn more about equity and diversity, you could try the writings of Dr Zuleyka Zevallos.
      1. https://othersociologist.com/otherness-resources/
      2. https://zuleykazevallos.com/about/
      3. http://www.latinorebels.com/2017/03/14/the-march-for-science-cant-figure-out-how-to-handle-diversity/
      Also...