Coronavirus is king - for now

Thoughts of a perplexed, ungroomed scientist in the times of a COVID-19 lockdown

In times such as these it is easy to get caught up in numbers. Exponential increases in things like virus infected people are really only supposed to be reserved for a bad movie starring Brad Pitt. On these occasions I always imagined I would be buried in science and I wouldn’t even notice the apocalypse. Turns out even my love affair with fact was to be threatened. I am exhausted.

Remember 3 months ago? When all we were concerned about was antivaxxers? Now we face a world without a vaccine and race toward one. I have several key thoughts and observations that have dawned on me while I sit, hair unkempt, at the computer:

1) People who are not qualified virologists suddenly are. Its amazing, it was the quickest set of degrees they have ever obtained. Somehow everyone mistakes their ability to use a search engine as the 4 degrees I have taken 10 years to obtain. This should not be confused with developing an interest in the subject. In fact, I hope the next 6 months opens the eyes of budding epidemiologists everywhere and we get a huge influx into STEM. This is more about impeding the dissemination of knowledge because you think you know better, Karen.

2) Don’t suggest to your co-workers that they turn their zoom camera on – you will see things you can’t unsee. In addition, is it just me or has the hadeda population decided it’s their time to shine the second you unmute yourself?

3) South Africa just recently introduced a set of laws to make the spreading of fake news a punishable offence. I have never been prouder to be a South African. Honestly, beats all the Rugby World Cup wins hands down.

4) I am busier than I’ve ever been with about 14000 applications, calls and papers to write and yet I miss the lab. Shortly, I will be back in there for COVID-19 research, and I know that I will miss my days of breakfast, second breakfasts, lunch, afternoon snacks etc. The grass is always greener on the other side of quarantine.

5) Tiger kings and tigers (also cats in general) can get COVID19.

6) Basically, all the reading I have done around the antibody work that I am about to start in COVID19 has not been peer reviewed. Does this concern me? Yes. Will I still read it? Yes. These are unprecedented times. In fact I think it’s kind of great that the science community is putting traditionally prestigious journals under a bit of pressure. Do I still want a nature paper? Yes.

7) The stream of science is hard not to enjoy. Many of us became scientists because of our curiosity and perhaps our inability to deal with social norms. But it is a thing of pure beauty to watch answers materialize where we had none before.

8) On a serious note, as South Africa enters its first extension of its lockdown, it is remarkable to me that people thought the government was legitimately going to ease the conditions now. Life as we know has changed. Travel will likely have to be put on hold until at least the end of the year. We will likely all be wearing masks in our daily lives. Until we get a therapy or a vaccine, we are held hostage by this virus. Countries who have eased their lockdowns too soon or were not strict enough, face huge ramifications. In a country that has many below the poverty line and many suffering with HIV and TB, we can’t afford to not lockdown. Of course there is always the terrible reality of our situation. Gender based violence is a staple in this country (hopefully the alcohol ban will curb some of this) but being trapped with your abuser must be some kind of hell. In addition businesses will collapse, unemployment will soar. These are all truly terrible but the alternative is really so much darker. Maybe we can bring the best out in each other. Donate to the solidarity fund if you can. Continue paying your employees if you can. Buy someone’s groceries if you can. Do what you can. Store your grain (or easter eggs) in your neighbours belly.

9) Isn’t it scary that we knew disease x would come from China and it would be a respiratory disease and wet markets were still allowed to proceed? How many other things do we know are inevitable? Climate change anyone? Maybe people should listen to scientists instead of an obnoxious man with an orange toupee. Ok, so hardly the I told you so we were hoping for.

10) This sucks and it is hard. It is ok to be unproductive and anxious.

Although I’ve ranted in this blog, I believe that people are at their core mostly good. I believe (and at times like these it is harder) but there are lots of things to laugh at and be happy about. For these things I direct you to John Krasinski’s latest effort to make us all smile SomeGoodNews – a youtube channel that tries to look for the good.

In the coming weeks I will do my bit for science communication and post some informative science going on to help us out, because let’s be honest – that’s all good news. This week, South African scientists reported the very first SARS-CoV-2 sequence from our country. This is extremely important, allowing us to see what the virus that causes COVID-19 looks like within our borders enabling us to track if and when the virus mutates. This might cause future therapies to become ineffective. The second vaccine trial has started in the US, following just 100 days since the COVID-19 disease was reported to the World Health Organization. Just to say this time frame is crazy. Vaccines take decades not months. But we had a good starting point – SARS and MERS (genetically similar coronaviruses) had already been studied in a fair amount of detail. We have done something we are used to in science; stood on the shoulders of giants.

Basically, we are stuck in this bad movie plot for a while. Settle in, grab some popcorn and be gentle with yourself and others. Also you don’t need to go to the shops 15 times a day, Karen.

#vaccineswork

Read more here!

Curiosity killed the antibody

The PhD condition

My PhD is fine!!!!

Crazy pet owner

Science is not a suggestion or a liberal agenda

Having been on hiatus for a full year, I should emphasize that I have still been writing, just on another blog for the South African Youth Academy of Sciences under the pseudonym Scientist Sim. Here is a link to the year that was 2016 in the life and times of a stressed PhD student.


In summary 2016 was this meme:

Actually for the world it was this:

I will now segway into the horror that has befallen the US. Specifically, the man who can not keep off Twitter at the moment; President Donald Trump.  A historic upsurge in world wide protest erupted in January and this is one of my favorite  posters from the women's march in Washington DC. 

The land of the NIH and swarming with female scientists, Washington was awash with demands that science matters. With a president that seems to take science as a silly suggestion rather than a friend of progress, there is a very real concern that Donald will reverse decades of good work. His attitude is portrayed in many of his strange actions.  The appointment of Steve Bannon as lead strategist went ahead even though he has published articles like “1001 Reasons Why Global Warming Is So Totally Over in 2016" even though it was the hottest year on record. The Environmental Protection Agency transition team was headed by Myron Ebell, a global warming denialist saying: 

 

The current head of the EPA is Scott Pruitt; another denialist that is in fact involved in a 28 state wide lawsuit against the agency he is leading. This is not the only area of science that Trump's small hands are stretching towards. 

In 1998, Andrew Wakefield published a case series in the Lancet, which suggested that the measles, mumps, and rubella (MMR) vaccine may predispose to development of autism in children (for an indepth review of this click here). Despite the small sample size of 12 children the paper received notarity, and MMR vaccination rates began to drop. In 2011 He was found guilty of fraud by picking and choosing data that went into the final publication and for ethical violations. He was later found to have received financial support from lawyers fighting autism cases. In my opinion, this man should have been arrested, but instead gets a documentary. Vaxxed-from cover up to catastrophe is, I'm sure, a labour of love from Andrew Wakefield that I will never pay to see. In a study involving 95000 children, no link to autism has been found; but clearly no one told Trump (A. Jain et al. J. Am. Med. Assoc. 313, 1534–1540; 2015). The entire basis of the vaccine/Autism agenda is based on this fake study-or rather the alternative facts represented. 

Trump has hired Robert F. Kennedy Jr, another denialist to head up the Vaccine Safety commission. He said this: 

 I would retort with this :

It is scary that in an age with all the information, the leader of the free world gets his news and his policy from conspiracy theorists. He views science as a footnote in what makes America great, and remains adamant that in order to "make America great again" one must ignore the people who have worked on scientific breakthroughs and instead turn a profit. SAD! 

There are gloomy days ahead. However, science birthed the light bulb and I refuse to believe that it won't continue to illuminate the world. 

How vaccine research is failing the youth

Being young in each decade means something different. Each generation has new challenges and struggles, new fashions, new pressures. Some things though, remain universal. In the 80s in this country the struggle referred to fighting an oppressive government and perhaps now it means a similar thing. We have bridged the gap between the 80s boomboxers and the millennials with a dark and ominous threat, HIV/AIDS and with no vaccine or cure in the foreseeable future, this looks to be set in. Despite this, we have come a long way in South Africa. From scandal that radiated from the division of AIDS in the early 90s (a ridiculous musical, a strange solvent turned injectable) to the early 2000s where our own president denied HIV causation and our minister of health “solved the world’s problems” with the African potato, we have been plagued with a series of poor political decisions. These have I’m pleased to say resulted in some great decisions; we have the highest governmental rollout in the world of ARVs and a mother to child transmission rate of less than 2%. We have great research culture in HIV too. Some of the brightest young minds are working on the best way to solve multiple problems. But vaccine research, now that’s a tricky business and it is really the only way to ensure a bright future for the youth.

I have just entered the world of HIV vaccine trials. I need to mention upfront that clinical trials are hard. It will take a minimum of 5 years to run safety and feasibility trials and product development is a nightmare. This is only after all the basic science has been completed which often takes a decade (monkey studies, idea development). But these are things that cannot be helped. So why do I say the vaccine field has failed? Vaccine trials feel very much like the blind leading the blind. Often decisions have been made completely out of line with sound scientific basis. There are many reasons for this, some more sinister than others. One is as a result of old dogma, which is a problem with science in general. There are almost always great innovations coming out from literature but people in the higher echelons make the decisions and sometimes they push their own agendas and sometimes they are nervous. Understandably; these trials use stupid money. A failed trial means lack of funding and more worryingly a dangerous trial means loss of faith in vaccines- something the world can simply not afford. The recent spate of measles related deaths is the US and polio-induced paralysis in children is a direct result of the anti-vaxxers movement. They are inspired by a paper, which has since been retracted for falsification, that showed a link between autism and vaccination. A lot of damage can be done by a poorly run trial but the misnomers that come from media are equally destructive.

Another argument for quick decisions within a vaccine research body can be made for progress for progress sake. This is important. We cannot wait another 20 years to get the perfect vaccine immunogen and we will learn from negative results. Having said that, we have to be going forward with new brave ideas. Some of them will fail but they won’t fail because they aren’t well conceived. We will head into the unknown but it should not be blindfolded or wearing blinkers. We need leadership that really gets it -that is not detached and far removed from the lab work, is not exclusively feeling the pressure of finance alone and is happy to listen to the bright minds they hire to run the trials and trusts them to input ideas.

The world is a scary place for the youth. 90% of the time we are in murky waters. We still have many of the same problems but we can’t solve them with 100 year old tools. We can no longer err on the side of caution and we can no longer allow politics to govern science. The field of science needs to start really listening and stop patting itself on the back for Nature papers no one ever implements into policy. Where is the application? Doing proof of concept studies with no measurable product in a clinical trial is a scary thought. What are we saying to the volunteers? “Please give us your time. If this works, we can’t give it to you because it is completely impractical.” We have to improve and we have to be better for those who are yet to come. We need to make it normal for the youths only problems to be a trivial shortage of selfie sticks or what to wear on Friday nights and not a fear of contracting a death sentence. A tall order-one I hope will be realised in my lifetime.

Bacteria horror

Hugs

Feeling lame

Pacman

Viral irony

Pablo-esque evolution

Le Inspirational

I recently met a personal hero of mine. I couldn't think of anything remotely intelligent to say and instead stood grinning like an overbaring Cheshire cat while we took a selfie. The only thing that I could think was she has a Wikipedia page. Clearly this is something Françoise Barré-Sinoussi doesn't regard as one of her greatest achievements: the discovery of HIV or the 2008 Nobel Prize for Physiology and medicine probably ranks up there. 

I wondered, while I stood there looking geeky, what she thought of these young PhDs gawking at her. In the speech she made later that day she said that scientists place too much emphasis on high impact papers. She said when you go to bed at night, papers that no one reads do not matter. At which point a bunch of people in the audience (predominantly clinicians and scientists) rolled their eyes; these people probably were also on a nature paper recently. She said that she tells her students to get out of the lab and to meet the people affected so they can look them in the eye and understand, not at a biological level but at a human level. That is where greatness is born.

I began to wonder if that is a lesson only learned by science's elite as they get older. Had she been awarded the Oscar of science at 25 say, how would her attitude be different? Filled with the folly and arrogance of youth or bolstered her to greater heights at a younger age? How much do these awards mean to the people who get them when they are only given 20 odd years after the fact?

Of course these mullings would all have been better things to think than "She has a Wikipedia page" when I met this great science mind. It is unlikely that I will ever be in close proximity to her again but with any luck, I will take her message to heart. Remember who you are working for. It is not for honour or accolade, it is for the people - past, present and future. A scientists reward: the selfish joy of discovery. And then there's a realisation that your tiny piece of information fits into an never ending jigsaw puzzle, the greatest one ever built. And if it doesn't fit, well, someone is bound to stand up and tell you that at a conference. Ah science, thy fickle beast!

B cell development: basically a romcom for the ages

I've always thought of our universe as a complicated version of one of the scenes from Men in Black. Will Smith peers into a locker containing an entire world of tiny aliens who think he's almighty because he is larger than them. What if all living things are really just small world's within bigger worlds within gigantic world's : worldception? Think about it: what if Bob the skin cell feels like he is just a cog in the policing machine for the man? Then one day he gets cruelly sloughed off just because you walked into a door. Supposing this is true, it should hardly come as a surprise that our cells' interactions very closely mimic our relationships or perhaps more accurately, a scene from The Notebook. 

Our immune system is a perfect example of the rollercoaster of love. They say that as soon as you stop looking for love it finds you. Well no one looks for disease and it finds our cells all the time. I never promised this would be a good analogy. Never the less the B cells have feelers out all the time, searching for meaning, searching for something to ignite their fire so to speak. Once they spot something they like, much like our version of brown hair or eyes that are as deep of the ocean, they activate. Secrete a bunch of things and start overreacting. Pretty much what happens to humans. 

Now although some B cells don't need any help to get to a happy chaotic stage much like humans, the majority need some company. And occasionally they need matchmakers. Certain cells provide T cells with an antigen or some attractive feature so that when a hunky naive B cell comes along they are ready to turn on the charms. Of course there are external factors at play, and certain factors drive the adonis B cells into different zones of the tissue. Think of the T zone as the awkward dating pool - the mesh of clubs, boring movies, sweaty hands etc. If the B cell doesn't find a T cell that matches what he is looking for he moves on. Likely to a place called the B cell zone. A place really where everyone hangs out and pretends they "don't need no woman" or whatever they tell themselves. In actuality what they are doing is just hoping to survive and go into dirt bike riding or some other crazy hobby until they again get sucked into the T zone. 

If the B cell does find what they like then they get trapped in the dating zone and they form a couple with the T cell. This of course changes both parties; for one once bonded it would be bad if the B cell went back off to scope out the rest of the T cell zone hoping for a more curvy possibly blonde T cell. Not only do they individually become pretty clingy but they strengthen their bond with reciprocal favours; bringing home flowers, washing the dishes, promising to fix the garage door. Eventually they form a synapse or as I like to call it, marriage. They move together out of the awkward dating pool and into their own place. Here they begin to divide and form a happy family called the primary focus. It is here that the sexy slim B cell often changes into a rather large flabby shadow of his former self, the plasma cell. However scattered throughout the home are cells that help provide complements (punny if you are an immunologist) to each of the cells and ultimately their marriage survives and they are average. 

Some B cells, like some people enjoy change and instead venture off into a new location with their partner. Here they change radically excelling in career and producing the best antibodies. Their partners change too. Occasionally there can be too much change and often B cells can no longer recognise the complements or attracting factors. Soon he's too busy working nights to notice Ben his eldest cell just apoptosed. The B cell is now barely himself mutating and hypermutating and now hangs out with his buddies in the dark zone. Sometimes the B cell gravitates back to the light zone once he has matured past his midlife crisis where he will be reunited with his T cell partner. Often the B cell and the antibodies he expresses have changed too little or too much and they must now fight for the affections of his partner or die. I realise this went medieval pretty quickly. 

Okay so perhaps not exactly like the Notebook - but still a better love story than Twilight. 

The PhD condition

I've heard of people spending 8 years finishing their PhD. When I was an overachieving undergraduate I would turn my wet noobish nose at these "lazy sloths of science". I mean clearly, CLEARLY these people were just sitting around the nespresso machine  and had never touched a pipette. Then I met science. Not the kind of science you read about in books, nor the kind in movies where lethal diseases can be vaccinated before the well groomed scientist in the heels rushes out to dinner with Brad Pitt. Science - the mysterious mush of the unknown. And everyday since I have been filled with the uncomfortable thought that it is out to get me.

I think I always knew I would be a scientist. When I was two I asked my dad where the light went when you switched it off. The feeling that I get when people ask what I do is a bit, I imagine, how Rocky Balboa felt when he reached the top of the stairs. I say imagine because I am not so skilled with the running thing, or the walking thing for that matter. " Ooh a scientist" they coo. "So what does that entail? "Then, as I explain enthusiastically I watch their eyes glaze over. But it doesn't matter for I am a scientist!

It was a natural progression then that I would do my PhD and about a month ago, I registered. But as much as I love what I do, I cannot shake the feeling of dread that I do not have what it takes. Science, it turns out is not just experiments and research and questions and answers - all things I am good at. Instead these things are only a tiny proportion of overall career. Much of science is being a glorified hobo begging the likes of Bill Gates for money. Slowly we add accountant to our resume. Not something I even remotely wanted to do with my life.

Then there is the never ending politics. If someone gives you a plasmid ( basically just a tiny nothing snip of DNA) and they are a big shot but did no other work for the project you were working on, they must be an author on your paper while someone else, who probably did a huge chunk of work gets bumped to acknowledgements because they only have a honours or something. Is it fair? Nope. Will it change? Nope. Getting bounced around by huge egos is they way it works and as your research gets into bigger journals so the pressure to bow down increases. Politician. Right, another thing I never studied.

Marketing is another huge part of research. So many Cell and Nature papers show obvious things. Things that are by no means innovative but they are repackaged  in the most amazing story. It's a bit like Shades of Grey. BEST MARKETING STUNT EVER. It's porn in Mills and Boon form; both of  which have been around forever; not innovative just repackaged. Generally scientists became scientists so they could be swathed in the warm comfort of no social contact. Instead we must become advertisers and more and more dolly our science up because bar charts are no longer enough. In fact infographics with 42 keys are the only way to go. Promotions....I can *gulp* do this.

It is not hard work I am afraid of, in fact I revel in it. However no matter how hard one works, it is never enough for the prying eyes of the PhDs  whose whole life is devoted to the lab. They eat there, sleep there, probably don't have a shower very often and then casually claim that anyone who is exercising or going home to a partner/child is simply weak. Having a life is just not okay. So as if all the pressure from the additional careers that we have taken on isn't enough, our own peers are constantly trying to undermine us. It's a  cut-throat world - and you just thought it was like an episode of big bang theory. 

The worst part of all this is that the two year old, the one who was so inquisitive about the world around her, is slowly receding into her shell. She fears speaking out lest her ideas be stolen from her or someone attacks her dreams of discovery. Galileo was killed by the church and I still think he had it easy.  

Tim Noakes-the joke? Or just an unfortunate rhyming name?

Tim Noakes is getting exactly what he wants. His book is sold out. Does he care that he has critics, including his mentor Lionel Opie? Probably not.

Everyone, bar those who are skinny, is hanging on to another pipe dream where veggies are just another thing swimming in butter. Lets think about it logically shall we? No carbs and no fruit. A fair amount of fat and veg. People lose weight. Do we know why? Can the man who developed this form of the actually ancient diet explain the weight loss? No. His form of comeback is actually that doubting Thomases "need to look around and explain how the low-fat ‘healthy’ diet we are currently promoting, is healthy and is not causing the epidemic of ill-health that began in 1980… three years after this ‘healthy’ diet was first promoted globally”. A nice bit of distraction. Why do we need to explain your diet Tim? Isn't that what scientists do? Aren't you supposed to do that bit?

My view on the diet is really neither here nor there. I mean people will do it because their mommies or their aunties have lost 6 kgs. And that's great. I mostly have 2 issues: 1) people are saying "read his book, he explains EVERYTHING". He explains what he wants you to know people. A cookbook, especially not one for sale, or something with revolution in the title is not a good enough source of information on which to base health decisions. Read his journal articles. Yes, you may be an architect or a bank teller and not get it first time round but really try. Or ask your friendly neighbourhood scientist to explain. Anything worth doing is going to take time.
2) The second issue is how this one scientist has managed to once again bring the whole of science under scrutiny. The people that are against his diet have evidence to back them up. He has evidence that his diet works but cant explain the mechanism. This is science. For every 10 references that you find for this low carb diet I can find 10 that say the opposite. Please know that this is NOT because science is unreliable. The aim of science is to refute each claim that is made. All scientists err on the side of caution. It is not "being mean" or "belittling someone someone". This is the only way science can move forward. Basically its a dogma eat dogma world.

And look, Tim Noakes is about to be a wealthy guy. When skinny people everywhere start dropping dead of  clogged arteries or diabetic people start trying to sue him because their condition didnt disappear, you know where he will be? In the Bahamas. With your money.

Cry the beloved country

This week I received some truly awful news. My inner geek pounded her fists, banged her head against a wall and screamed in futility into a fluffy pillow. South Africa is officially the lowest ranked country for science and maths education and the third lowest for overall education out of those involved in the Global Information Technology Report 2014. So that is 148 out of 148 and 146 out of 148 countries, behind Haiti. Haiti, the country devastated by one of the worse earthquakes in a developing country. Fantastic. I honestly feel like my puppy died. My wonderful scientific puppy. 

The government is the predominant party to blame here, but that's the obvious thing. Out of 148 countries we ranked 119th in the ability of our government to procure technology, 105th in the tertiary education gross enrollment rate and 116th in internet access in schools. But I think I'm more depressed by the apathy of students in this country to maths and science.

If you constantly convince yourself that something is too difficult for you, it will always be impossible. Likewise, if you are a parent and you reinforce the notion that maths is an alien language sent to suck our souls, don't be surprised when your kid fails it. For some particular freaky people, maths is the shiz-niz. Maths is the same in every language and in some ways that is really comforting to some. To be honest I can't remember if someone told me that or if it was a particularly cheesy line from Mean Girls. Probably the latter. 

I never had a philosophical relationship with maths. I, like most scientists, even like the man who invented calculus,view it as a means to an end. Maths was mostly developed to further science and unfortunately almost all of our understanding of the world is based on physics. Unfortunately for me, I don't like physics either but diligently I studied, always looking to the bigger picture. One day I knew I would be able to say to random people, "Hello I am a scientist" while wearing a HAZMAT suit in a biosafety level 3 facility. Which you have to admit, is pretty hardcore and a bit more exciting than "Hello, I'm an accountant, look at my spreadsheets".

Every day I learn something new. Every day I am forging ahead with a new exciting idea. Everyday I fit another piece into the puzzle. And its great, truly the best thing ever. It angers me when people say "Oh wow, you are so clever to be able to do what you do, I could never do that." Well to be honest, first I feel flattered then I try to get them to say I'm pretty too. But the bottom line is that anyone can do it, if from a young age they are given the bug of wonder; the urgency to ask questions and never stop asking them just because your parents want to kill you or because there is something bright and shiny on the TV. I also acknowledge the fact that in developing countries we are dealing with way more than just problems in schools. Our society is very broken; filled with needless violence and cultural clashes but that does not mean that we can accept mediocrity. We can not say that because someone got 30% for science they pass. I mean if you know 30% of chemistry, you may drink H202 instead of its non-lethal common counterpart. We can not accept apathy because, lets face it, the rest of the world is laughing at us. 

The message if you are a teenager is life does not end at 15. If you can't go to the one direction concert because you are studying for a maths test, it won't kill you. Another boy band will come along, probably with the same songs in 20 years time. And do you know what? You could ride into that concert on your very own T-rex. Science-it's real. 

If you are a parent, please stop telling your kids that science is hard. Of course it is. Anything worth doing is hard. So is anything not worth doing, like being a street sweeper or cleaning toilets. Science is fascinating. And there is so much more to find. In the great words of Ellie in Up "Adventure is out there, " don't stop your kids from finding it.