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Community is Communication – #JoelKallmanDay October 11, 2021

Posted by mwidlake in Friday Philosophy, Perceptions, UKOUG, User Groups.
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My life is not just Oracle and the Oracle community. I’m part of a couple of other communities as, I hope are we all – be they your hobby, an interest or pastime, the church, your friends. And the key to community is, I feel, communication.

2 days old

I was thinking of this a few weeks ago in another, important (to me) part of my life, which is fostering cats for a local pet charity. I’ve had cats for most of the last 40 years of my life and I’ve missed them since our last one died about 6 years ago. For a mixture of reasons we decide that rather then get another “forever” cat we would temporarily look after cats that needed care before being rehomed permanently.

We’ve had several cats now and it’s something we enjoy doing. What has not been so good, at times, has been interacting with the staff at the charity. There have been several situations where we have tried to contact them and either the reply is slow to come or does not happen at all. We do understand that they are often dealing with a fast moving or unclear situation and, especially with Covid-19 at times effectively removing most of their volunteer staff, more things to do than they have hours to do it in. But when you are asked if you can take on a new cat in an emergency and you drop your plans to do so – and then hear nothing for 3 days before being told “Oh! No, we organised to support the current owner in keeping it”, it’s… vexing. Especially the third time in a row it happens.

It nearly made us give up on them, the communication was just so lacking and poor.

2 weeks old

But to balance that, there is an online facebook-type group for all the fosterers and they are much better. We put up pictures of our fosterlings, swap tips, and generally support each other. It’s good communication. I say this despite a lot of the communication having a tone that just is not me (“Ohhh, isn’t paddy pooky so *cuuuuute*! It makes my hearty warty ache!”). However, that’s more my problem than theirs and in fact I modify how I say things a little to suit the general tone (Mrs W looks at some of the things I put on there and says “YOU wrote that?!?!” – yeah, it’s the style they like).

Similarly communication is vital in our Oracle communities. From organising an event to letting people know what your user group is doing, communication is at the heart of it all. Part of it is simply having some communication. If you never hear from a group you are involved with it is, just like with a friend who never gets in touch, hard to maintain the interest. Lack of communication can kill a community really quickly.

On the other side of the coin, over-communication is not good. When I was president of UKOUG one thing I pushed for was for us to communicate with the membership a little less. We used to send out monthly updates and also lots of emails about events and other things. It was too much, I knew people who simply ignored any email from UKOUG as it was endless. I don’t think we got it quite right when I was there, but we altered things so that fewer emails went out and they were more varied. Instead of a monthly update there was an update from the CEO one month and one from me as the president on the other month, with a different flavour and a modified focus.

3 weeks old

The final killer is empty communication. Saying stuff people are not interested in or saying “great things are coming” but nothing substantial about what that great stuff is. Teasers are OK but only if the tease gives a hint of what the new, cool thing is (and it actually is new and cool – so many commercial things are decidedly not cool, let alone interesting, and telling us you are excited about it makes me question how vacuous your life is…). Repeatedly saying “great things are coming” but not what they are sends a clear message of “we have no idea what we are going to do but don’t want to admit that”. There have been a lot of issues with that until recently with one particular Oracle Community area. It’s improving but they have a lot of work to do to make people reconnect with them again.

I love the communities I am in. I am passionate about the Oracle communities I am part of. If I want to help keep those communities vital and active, I need to help with the communication. I can’t think of a single community I am in that I am enjoying where communication is not at the core of it.

This post is part of the #JoelKallmanDay and, if you knew (or even just knew of) Joel , you will know why I chose this topic. Joel was a passionate, effective communicator and a rock within the APEX community.

Friday Philosophy – Early Mistakes Uncorrected Means Poor Final Systems August 13, 2021

Posted by mwidlake in Architecture, development, Friday Philosophy.
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A few days ago I fitted a sink (hand basin) in my garage. Bear with me, this IS related to I.T.

It’s maybe is not so clear from the pictures, but that sink is at an angle (see the spirit level in the second shot, that bubble is way over from being in the centre), leaning back towards the wall on the left. And the splash back is also not straight, it is a good 5 degrees from the vertical. I’m pretty good at DIY – putting up shelves, building cupboards, fixing furniture, building the odd bit of wall, erecting & insulating sheds (which I take power and lighting down to)… And I am very, very meticulous about things like getting things straight and level. As I progressed with the job of putting up this sink and reflected on the process, it so reminds me of several application development projects I’ve been involved in (or was brought in to help crowbar back into shape)

Where Did I Go Wrong?

I’ll add some pictures to the bottom of this blog, but for now I’ll just describe what happened. When I offered up the sink to the wall I realised that the pipework (put in by competent builders but with no real consideration of my planned improvements) was exactly where the sink should go. And I also realised that even if the sink was put higher (way too high for me) or lower (well to low for a normal heighted person) the pipework would still be an issue. Also, the back wall is not quite vertical and the two walls are not quite at 90 degrees. This sort of thing is not unusual in any building (though slightly vexing in something built only 12 years ago) and to me it’s like the not-quite-perfect situation most application developments start at. You might not be using the best database for the solution, you might have to use a computer language that is not the best but you have staff skilled in it. There will be bizarre parts of the application you are replacing that you have to keep as the end users have got used to them – or even built business processes around and no one wants to change those now.

Good developers and systems engineers can work around such issues. A good DIYer can take into account badly placed pipes and wonky walls. I could have cut out and replaced the pipework – but it would have been a lot of work and I am not very good at plumbing (which is why I use push-fit plumbing: less neat & more expensive, but dead easy & quick). This would be like changing those slightly crazy business practices forced by the old system for ones that would benefit the business eventually, but it’s a lot of effort to change. As for the wonky walls, sorting that out would be like re-skilling or replacing my whole development team to move to better technology – Possible, but not going to happen.

The pragmatic solution was to mount the sink on wooden battens and make the battens thick enough to avoid the pipework and allow me to correct for the wonky walls. A cheap, pragmatic solution to the imperfect starting conditions.

Only, I messed up. I spent hours first doing the extra plumbing work to get an isolation valve beyond where the sink & splashbacks would be (so the water could be turned off for maintenance or leaks), and a feed for the hot water unit to come. Then I failed to plane off the battens for the sink properly and they had to come off and be messed with several times. When it came time to mount the sink, which goes on two metal pegs, I screwed one of them in too high. Bloody hell.

From this point on – I was doomed. I should have taken it off the wall and tried again

I was tired, annoyed. To fix the peg I would have to replace the batten. I did not want to take that sodding batten off the wall and replace it (it had been the hard one to make). It was also the end of the day. So I did a “bodge job” – which means a quick and poor quality alteration to get you past a problem. I packed out the space between one mounting peg and a guessed proper height for the sink. I replaced proper planning and good development with something you throw together at the end of an Agile Sprint, so I could meet my objectives and go home.

The next morning I realised the sink was more than a little uneven – but I decided to continue. And that was it, I had messed up the whole job. In my head I thought I could modify the upright battens, get a little leeway with the tiling and grouting and make up for the “bodge job”. I won’t bore you with the full details but I was so utterly wrong. What would have been two totally square and vertical battens for one splashback and a pair of slightly trimmed for the other turned into endless alterations and re-working, especially as towards what should have been the end of the job, it was obvious the tiles were going to look awful (good tiling is all about straight, parallel, horizontal, well squared lines – they magnify imperfections, of which I now had many) so more reworking was required.

If I had fixed the sink mounts first thing that morning, I think I would have finished the job in that same morning, not one and a half days later.

It’s Not The Starting Conditions, It’s The Cutting Corners

The more I have thought about that sink, the more it echoes what I’ve seen in the world of computer application development.

Many times, when the development of an application has gone wrong, I hear people blame the starting conditions. “We had to use Java Struts” or “The analytics team demanded they could query anything” or “We had to make the system talk to the old warehouse system on Informix” or whatever. I doubt these starting conditions were really a big problem, you knew about them and your design should have taken them into account. A good designer will plan around them, a good developer will code in an interface, a good DBA will add in the required indexes.

Not properly planning the system or not prototyping the solution will invariably lead to disaster. In my sink scenario, that would have been the case if I had not used my experience and thought about the long term and decided to try to attach the sink to the plasterboard walls directly, just under the pipework. I’d never have got the tiles on and the sink would have fallen off the wall very soon. I’m not saying you don’t see this failure to plan upfront in application development, it has sadly become more common. Too many places think “Agile” or similar is just hacking the system together and fixing what is wrong. That is, to use a coarse term, just bollocks. Agile only works well (in my experience) when done on top of a very good design, created by skilled people. It’s not easy.

However, the most common cause of issues I have witnessed, by a long way, is that of “bodging a solution” – and again it is very strongly associated in my experience with “agile” done wrong, or even worse the “develop to fail – and then fix quickly” mentality. Yes, you will get something that works. Very quickly. And it will probably be an “uneven sink”. It will do the job (hold water, let people register for an event) but as soon as you try and extend the system, it gets harder and harder and harder. And you spend more and more time working through that technical debt you inflicted on yourself. And the end result will be very much sub-optimal. OK, a simple thing will be fine when put together like this (a shelf to hold photographs, a simple calendar app) but a complicated system like a hospital patient administration system or a fraud detection application, a whole bathroom refurbishment… It’s going to be a mess. I’ve seen and suffered from this cascade of crap so many times over the years.

The whole idea of things like sprints, where you are put under tremendous pressure to just make your bit work, causes a lot of bodging of things. Yes, it does, I’ve seen it. I’m sure if things like code review, pair development, and periods of planning are put into Agile (like they are supposed to be) the bodges could be un-bodged. But I simply don’t see this. And the whole “fail fast and fix” idea seems to me to absolutely guarantee a system covered in duct tape and almost unmaintainable. All for the sake of get it done NOW.

I learnt many years ago in I.T. that it is far more efficient if you fix the mistakes when you first see them and fix them well. Always build on a stable base and keep it solid. Otherwise, as you progress, the pain just builds and builds and builds. This latest DIY experience just hammered it home.

The sink I put up does work. None of the pipework leaks, the splashbacks do not have gaps to let water in, the tiles are aligned (mostly), they are high enough to catch splashes. I know I can put the water heater above it… but it will be higher than I would want and if I do not make it lean to the left, it will make the sink look even more skew whiff. But by the end I put in twice the effort (if not more) than I needed to in order to have a functional sink – and it looks weird.

Do not bodge the beginning of a project, make it right and save yourself from endless pain later on!

For the interested, a pictorial progress of the job.

Joel Kallman, The Heart of APEX, Sadly Gone May 28, 2021

Posted by mwidlake in Uncategorized.
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Important – If you have come to this post because you were directed here by one of the several covid-19/vaccination denialist sites that are trying to use the death of Joel to support their position, then this page is not for you. Please go back. This page is about the death of a nice person, who died of a disease he tried to do something positive to combat.. This post will not help you, it’s not part of your echo chamber.

If you think that the death of just one person amongst the hundreds of millions vaccinated is significant in respect of vaccination, then I’m sorry to say this but – you do not currently understand medicine, epidemiology, immunology, biology, or really science. And this post won’t teach you. Other posts on this blog might (search on covid-19. *Update* I can see that almost no one has bothered to do that search). I allowed two comments on this post and replied on the topic of why you can die from a disease you have been vaccinated against. No more comments will be allowed as this post is an In Memoria piece and not somewhere for people to try and make their point (update – why are some of you still trying to comment? Duh!!!). If you want to understand more about SARS-CoV-2, vaccination, or epidemiology, I suggest you read proper, scientific articles about it. Try Wikipedia to start, look at the NCBI or the NHS sites. From there go on to scientific pages, those by people who’s actual profession is to try and understand all of this. And if you think all those places are part of some great plot of deceit, then you have bigger issues and nothing I say will dent your faith.

As I said, this blog post is not for you, please go back to your chosen view of the world.

Now, for those of you who knew or cared about Joel Kallman please read on….

News is spreading around the Oracle community, and especially the APEX community within it, of the passing of Joel Kallman from Covid-19, at just 54 years old. Joel, along with Mike Hichwa, created APEX in 1999 and since then he has been passionate about using it for the betterment of anyone and anywhere he could find a use for it. But more than that, Joel has been passionate about community. APEX is the technical product he is known for, but everyone who met Joel knew he was, more than anything, passionate about people and doing the best for everyone.

When anyone in our community passes away there are tributes paid. But I don’t think I’ve ever seen so many and with such depth of feeling as there have been for Joel. Everyone who met him seems to have their own story of what a supportive and kind person he was.

So why add my own, especially as others knew him better and have better memories to share? Because it’s another candle to the shining beacon of remembrance that Joel deserves.

My story of Joel

I didn’t know Joel very well, we had exchanged a few words at various Oracle conferences but never had a proper conversation. However at OOW London 2019 he came over to me, almost jogging through the throng calling me. “Hi Martin, I’ve been looking for you – I’m Joel Kallman”. As we had briefly met a few times and he is so well known I did wonder why he introduced himself. But then I’m not always good with people, but Joel was brilliant with people.

He wanted to write an article for Oracle Scene, the UKOUG magazine. We (well, mostly my predecessor) had asked him a few times in the past but Joel was always really busy. “I know I keep turning you down, but it’s on my list this year to offer you something – would that be OK?” Well hell yes! He’s Mr APEX and I knew he could write well. It would be a feather in our caps to have him write for us. I was actually on my way to meet someone and I suggested to Joel we meet later but he said no, he had no idea when he would get time again, “ Let’s sort it now, I will walk with you”. And he did, for about 10 minutes, away from where he needed to be. And he was not so much interested in talking about the possible article (that took all of a minute), but more in saying really nice things about UKOUG, how he appreciated me taking on being president, saying it was so good that people like us helped the community and asking me how it was going. That 10 minutes made me feel really good.

In the end the article for Oracle Scene did not happen. That’s not unusual, we are all busy and Joel more so than most, authors often let us down at short notice. But the way he handled not being able to do the article was unusual. Joel was blowing us out with only about 2 weeks before copy date (again, not unusual). But he insisted he have a video call with myself and the editor to explain why he could not do the article and to apologise. The irony? Joel had cancelled the article as he had been working 18 hour days, 7 days a week, for weeks to get a prototype app and the supporting infrastructure together to track Covid-19 symptoms and what drugs people were taking (all drugs, for any other illness, to try and spot a correlation and thus a potential drug target and potential treatments). Some of you may remember Oracle making a huge thing of that app. Joel had poured all he could into it as he thought it might help everyone.

To be candid, Joel looked incredibly tired and he said he’d not seen much of his family for a couple of weeks, but he took time out to do this for us and he must have apologised 4 or 5 times. We were saying “Joel! It’s OK! Go get some down time!”.

Such a nice man and such bitter irony that he died from Covid-19, something that he put so much effort into tackling.

Other Stories And Words.

As I said, so many others have wonderful things to say about Joel. Liron Amitzi has a lovely story about Joel going that extra step for his audience. Connor McDonald shares how Joel explained his ethos of raising up those around him and how maybe some good could come from the awfulness of Covid 19, plus a link to an APEX community page we can all leave our stories on.

And Lauren Cohn has put together a really touching video of Joel, including the personal request he made (which Connor quotes), which starts at 1:38) in his last keynote about us all being part of our communities. I think that video might become his unofficial epitaph

{I’ve had a report (thanks Steven) of the above link not working so try https://vimeo.com/556008201 if not}.

I’ve said a few times about my thoughts on community and being there for others. Joel not only said it but did it, and was an example of kindness and his passion for doing the best by everyone. He was certainly someone to look to as an example. I’m wishing I knew him better,.

I’ve Decided What I Want, Now I’ll Pick My “Science”. May 20, 2021

Posted by mwidlake in Uncategorized.
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This post is, I’m afraid, a rant. I let rip on social media (Facebook) about something that has been annoying me about some people’s attitude to Covid-19. A couple of friends don’t use FB and said they wanted to see what I wrote, so I’m repeating (and expanding) it in this blog post. Stuff we put on social media quickly drifts into history and out of sight (it’s often still there but no one looks at it) but blog posts tend to live on, so this post may get taken down in a week or two.

Sometime you just have to let it out…

So, what did I say?

Something I have noticed over the last 10 years (OK, 15 months really) is that what many people state about Covid 19 and all the rules & restrictions is generally dictated primarily by what they want for them – and is sod all to do with the societal need. They have already come to a conclusion as to what they want to happen and then they will pick “science” (which is often not science but more what other people, with or without any biological or scientific skill, have said) to support it, or cite “well it just makes sense” or “the rule stopping me doing this is just ridiculous”.

If keeping us all safe means limiting personal contact then personal contact businesses don’t agree (how many of us REALLY need a hair cut, let alone our nails decorated with glitter). Yes, you might like going to the gym or want a new tattoo but that’s a want, a desire. Not a need. Compared to increasing the risk of spreading Covid-19 and once more seeing our health services having to yet again go the extra mile (or 10) and cancel/postpone all the other stuff they do, your want is rather selfish.

If we are told not to move geographically in order to slow the cross-pollination of SARS-CoV-2 strains between regions then many people from holiday based companies & venues scream that travel is not the actual problem. Yes. Yes it is. Most of us have never before had real-world experience of epidemics & outbreaks of highly contagious, potentially fatal diseases (like SARS & MERS or outbreaks of other contagious diseases) as this is the first pandemic (world wide epidemic) we’ve had for a lifetime. But stopping movement and isolating the ill is about the only way to stop such diseases, aided significantly with vaccines if available, and is a common when such outbreaks occur. I think this lack of personal experience is part of the problem, most people have not had to go through it before so they struggle to accept it is needed now. It makes it even harder to accept because, on an individual level, Covid-19 is not actually that fatal. And if most of the people you know are young, you don’t “see” the impact. Population wide, it’s awful. Go chat to a hospital worker, they’ll tell you. Or actually look at the articles on what is happening in parts of India. It’s bloody awful.

But a lot of people want to go somewhere, or their income is dependent on people doing so (which is much more significant than a theoretical risk, isn’t it?) so they decide what they want and then pick the opinions/science to suit. It really helps if government helps those impacted financially, which the UK has sort-of done, but could have done better. Doing so helps remove the immediate, personal threat and allows people accept the wider, actually more significant societal threat.

If preventing new variants coming into the country means limits & forced isolation for travellers – travel companies disagree. What a surprise. And the screams when it is suggested people will not just be asked to self-isolate but will be checked up on and punished if not. Let alone made to stay in isolation in a hotel. If you *really* need to travel, so to see to a relative’s medical/care needs, it seems people are willing to accept the rules as, compared to the serious need for the actual trip, it’s just an imposition. Popping over to Tuscany for some sun but then being expected to stay at home to protect the nation is seen as an over reaction to such a frivolous thing. Maybe the problem is not the “over reaction” but the frivolous part.

People living in rural communities that have lower levels of transmission “than those oiks in the towns” want to be excluded from the local towns when it’s decided a region needs local controls. “They” have the problem, don’t include us! Well, boundaries have to be decided and they have to be simple. In the UK we have had at times just too many areas with different rules and no one is really sure what the rules are for where. My area is Uttlesford and it was level 3 when all around was 4. Have you any idea where Uttlesford is? And it’s boundaries? Didn’t think so. I live in it (so I know where it is) but I don’t know when I leave it and go into Braintree. Every time rules are based on an area which is not really well defined (like a national border) it’s confusing and there are lots and lots and lots of borders. Then people scream “Unfair!!!” about the borders. “Why can’t I go to the pub, but that bloke down the end of the road can!” Because the border has to be somewhere, and wherever it is, there will be people on different sides of it under different rules. It’s an unavoidable consequence of local rules OK? And on the topic of the nasty town where all the disease ridden people are and only they should have the restrictions. Where do you go to shop or get the car serviced? That nasty town. And they probably account for a large part of the financial input to those oh-so-pretty villages which the locals want to keep for themselves.

And the one that grinds my gears most is “It’s my Mental Elph!”. It’s replaced “I know my Rights!” as the cry of the unknowing as a demand for stuff they want. “I want to be able to do X as not doing so is harming my mental health”. Well, laying in a bed for a week tied to a mask keeping you alive with high pressure oxygen sort of takes it’s toll too, as I remember.

Mental health is a serious business, it can be utterly debilitating, life-altering, even fatal. Being sad, or bored or not able to do what you want THE VERY DAY you want it is in no bloody way the same as a chronic mental health condition and is not a threat to your mental health. Just stop it. Mental Health has struggled to ever be taken seriously and, now that it really is getting more attention and justifiably viewed as an illness to treat and not a failing, this almost knee-jerk “it’s harming my mental health” is, in my opinion, belittling a serious issue. Or more accurately a set of serious issues as, like cancer, mental illness is not a single disease but many. But every day you will see someone on TV saying it as a reason to be allowed to do what they want. You wanting 2 weeks shagging in Tuscany is not even comparable to someone asking if life can get any more shit and struggling to function in society.

So many people decide on the “science” and “what is fair” based on their personal desires first and foremost. Not what will give most people the best life they can have. I.e they have not read a single sodding article on “the science” let alone checked out if the references even lead to a real scientific paper. It all just ticks me off. Any time you want the rules about Covid-19 to change, ask yourself a question. Do you just “want it” for you? Or do you want it for the people around you? If it is just for you, fine! But be honest! It’s OK, you want it. But don’t try and make out you want it for the common good. As, chances are, you don’t give a hoot about Janice down the road. Go ask Janice. She don’t want her nails painted or to go to the Algarve or have a rave. She’d really, really, really, like to see her daughter for a hug and go to Bingo. But she’ll stay at home alone another year to “protect the at risk”. Which mostly, it seems to me, more and more consists of a people who will bend all rules to suit what they want FOR THEM. Which is where I started…

So why am I ranting about this now? In the UK we are doing really well, cases are down, deaths are down even further, things are opening up and OH BOY am I glad they are. I want everyone to stick to the rules to protect society but what I really want is to be in a situation where we don’t need the rules. And if everyone had stuck to the rules, and our government had brought in the rules when the epidemiologist and medics told them to rather than later, we would have gotten rid of the rules sooner. And less people will have died or been harmed.

World-wide things are generally improving and more vaccinations are being administered, surely it’s all good?

Well, biology is complex and it’s a sod sometimes. Even as we reduce the limitations in the UK, more and more people seem to be behaving as I’ve described above and demanding what they want, not what is sensible. And there is this new variant from India and it’s a bastard. It’s even more infective than the Kent variant and that was a swine, so I think we might see another increases in cases. Hopefully the vaccinations will mean serious illness and deaths will not rise in the same way here in the UK, but I think we are not out the woods by a long way.

I told you it was a rant, sorry.

Running Courses In Covid Times April 23, 2021

Posted by mwidlake in Uncategorized.
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I’ve been running courses in I.T. on and off for my whole career – which is getting to be quite a long time now. It’s probably 30 years since I ran my first course, teaching hospital staff how to use the patient administration software I helped to develop.  Of all the things I do, running training courses is probably the part I have enjoyed the most. But it is also the task I find most demanding & draining. Doing so remotely, as is the only option in Covid times, is something I find even more of a challenge. For two whole months this year I ran a course a week, all remote. Below, I’ll explain why I find remote tutoring harder and a few things you can try to make it work a little better.

ScreenHunter_ 672

 

It’s much harder than a conference presentation

I think anyone who was ever taught classes (let alone been a real teacher!) would agree that, until you do it, it’s hard to appreciate the emotional & mental energy it takes – even if you are teaching a topic you know inside out, upside down & back to front. If you’ve presented at a conference or similar, you know how much that can take out of you. Doing a course for a day is like doing a dozen such presentations. Yes, a day’s teaching is probably only 5 or 6 times as much presenting time as a 45-60 minute talk, but it’s the lack of recovery that makes it so much harder. Pretty much anyone can walk  4 or 5 miles. Running it takes some dedication but it’s not too hard to build up the fitness and stamina. Doing a Marathon? Totally different proposition. I really, really respect people who can teach all day, every day for 5 days, then do it the next week, and just keep doing it week after week, year after year.

 

It’s that lack of Interaction

OK, so I’m saying teaching is hard and you may or may not agree, but why do I say it is so much harder remotely? Because being remote and communicating through a screen removes 90% of the interaction between myself as the presenter and the delegates.

When I am stood in front of 12 varied human beings talking to them about how indexes work, if I am doing it the way I like to do it, there is a constant two way flow. I don’t mean they are talking back to me (although that is great and it does happen more face-to-face) it’s more I can get a feel for if the delegates are understanding the topic, if most of them already know this, is anyone lost.. have I just said something that does not make sense? That’s a good example actually, the power of detecting you just lost some of the audience. Often when I have taught people there will be someone (or someones) who’s first language is not English or they did not grow up in the UK, so if I use a colloquialism or make a reference to popular or historical culture, they may not get it. We all do this all the time, we assume that if we make a humorous reference back to a kids’ program then everyone will get it. Which they do if they grew up in your country, even usually if it was 2 decades later! I’ve tried to coach myself to not do this, but then sometimes these cultural references back to something outside the course material that most of us share helps us all relax and get on. So making the references are generally good – but you have to catch when it fails and “mop up”. Real, physical interaction makes this easier.

With a physical course I can judge if someone is not understanding and I do not need to ask “Phil, do you need me to explain that again?”. I simply would not do it that directly in a physical course, it is putting Phil on the spot. I’ll see Phil is perplexed and I’ll explain to the whole class again and watch Phil to see his reaction. With remote training, that feedback and how you handle it is greatly reduced.

The other part of physical courses is that when you have a coffee break or stop for lunch, you are usually all spending time around the terrible coffee & nasty sandwiches provided and you chat – like normal human beings! It’s a lot easier to communicate with people if you have some rapport with them and those breaks are vital to that rapport. Again, it all goes when you teach remotely. As soon as you break for a 15 minute loo-and-refreshment opportunity all screens & microphones that were on are off. I’ve tried staying at my desk, seeing if anyone else stays to chat, but it almost never happens. Besides, eventually I need to nip off for a pee, make a cup of tea and stroke the cat and if I’m talking to someone 1:1 they can take umbrage at this! When you are stood in a group in a physical room chatting, no one minds when I run off for for 4 mins.

I learnt early that anecdotes, especially if they make me look like an idiot, really help oil the wheels of social interaction – and will prompt at least some of the delegates to reply with their own. And I also scatter in some anecdotes that could be classed as bragging, but I am “the trainer” and it helps if they feel I am someone who knows their stuff via actual experience and I have done things for real and not just learnt training material or read stuff.

But hopefully you get the point. Physical presence allows the trainer and delegates to communicate and the trainer to control the flow of information. 

What are the delegates actually doing?

The other downside of remote training is loss of control. With remote training the delegates can do what they want – and most of them think I won’t notice. Of course I bloody well notice!

Of course, it is up to me to make the course as engaging and informative as I can and I do try, but sometimes it’s hard to make some of the necessary material “zing”. I’m sorry, understanding Oracle object statistics is just fundamentally dull, but you cannot understands how to do SQL performance tuning without that knowledge. It’s natural for people to drift off a little during dull-but-necessary bits.

ScreenHunter_ 673

When I have bodies in a room, I can tell very, very quickly if someone is reading email or surfing the web. In such a situation I’ll try to use subtle communication to stop this – looking at them, making a non-specific comment about “you get the most out of training…” or even asking them a direct question, as if I picked someone at random.  If I have the control, I’ll make it harder for people to goof off during the course – I do recognise it can start as something people do “just for a minute” or to check something they are responsible for, but it’s opening the door to distraction.

Fundamentally, If you are in my course, someone has paid for you to be on the course. And you either asked to be on the course or it was deemed appropriate for you to be on the course – deemed by your management/employer who is paying for *me* to be giving the course and for *you* to suffer it! Frankly, I don’t care if you do not turn up at all – but if you turn up, blank sessions & then ask questions that you would know the answer to if you had been engaged, you are now not just wasting your time (and the money paid by your employer) but also damaging the worth of the course to those who want to learn. I’ll have to take time out I could spend on the other delegates to drag you back up to speed.  People like that f**k me off. Sorry

I have kicked people off my courses if I feel they are detrimental to everyone else, but I’ll maybe talk about that at another time. The key things is, in a remote situation I loose a lot of my ability to spot people drifting off or address it.

So what can you do to improve remote training?

1 – you need interaction

The first thing is to encourage (and then if necessary insist) people have webcams on. You do not need *everyone* to have their webcam on – but I sure as hell now know that if no one has a webcam on it makes you feel like you are presenting to a brick wall. It kills the flow. Many people just don’t want their camera on (some people working from home barely wash or dress, some do intend to goof off and so do not want to be seen doing so, and one or two have become really self-conscious as 8 months in reach of endless biscuits and no hairdresser has had an impact). A mistake I made at the start was not encouraging more cameras on.

Ask questions of them. It can feel a little trite and sometimes no one wants to answer questions like “what do you think will happen if…” but you have to do so and then wait them out, until someone answers! Even better, get a few discussions going. It does not really have to be about the course material, but of course it helps if there is some relation to it.

As I said, no one seems to hang around during breaks or lunch. And some bugger is always late. So alternate between having a little chat for the first five minutes of the next session (about  *anything* – “My cat has just thrown up”) to get that interaction going, and starting the material dead on time when the next session is starting, to discourage tardiness. If someone is repeatedly late I stop answering if they ask a question on what they missed.

2 – pretend your web cam is a friend

Most people (including myself) can start to talk in a fast, dull monotone when there is no feedback. And you talk at what you are presenting, the screen with your slides or demo on. It’s not an engaging way to present. One thing I don’t think works (counter-intuitively)  is to put the presentation on the screen your web cam is built into or attached to.  It’s not like a TV camera, the web cam is right up to you. You might think you look like you are looking into the web cam but you are not, you look like you are staring at the chest of your delegates (if they are in front of their screens). You are presenting in a dull, boring monotone, staring at their chest.

So talk TO the web cam. Look at it, train yourself to present to that black dot. And imagine you are explaining this to a mate in the pub. I did wonder about putting a picture of someone I find attractive above the camera to remind me to look at it, but no one wants to see the presenter drool. When you are describing what is on the screen, it’s OK to look at *your* screen, not at all at the web cam, because the delegates are looking at their screen. But when the focus is not what is on the screen, turn to the webcam, to your mate in the pub.

After 2 or 3 hours of this with no real feedback, your own energy levels will probably drop, no matter how hard you try. Fluctuation in tone, willingness to make little jokes & asides, it all dies off – and your presentation style becomes dull, flat, and (frankly) shit. After 3 or 4 days? Awful. This is another part of why you need feedback. I in effect ended up presenting to those who kept their web cams on or were asking questions. On each course I managed to get at least one person to turn on a camera and I gave THEM the course. The others? Well, yeah, they were there I suppose, but I gave the course to Michael or Cali.

And visual feedback is way better than aural. I would rather have people on mute but visible than people I can hear and not see. Apologies to the blind community, but I sure as hell get more out of visual feedback to sound. With sound there are times when all anyone can hear is someone breathing hard into the mic, someone having a coughing fit, someone eating a packet of crisps. A discussion with a partner about the bins, another about why in hell do we have no milk it was your turn to buy milk…. And, sometimes, sound I think I never need to know the source of, but it should have been muted, OK?

3 – Short days, lots of breaks.

An 8 hour day of training in the flesh is hard work – and that is when you have little breaks when you all go over to the refreshments, or queue for the loo, and chat. 8 hours on Zoom or whatever, as many of us have learned this last year, is a destroyer of souls and any will to keep breathing. When I agreed to do these course I said right up front that it would be done in half-day chunks, I’d learnt the hard way that more than one day of solid remote learning is unpleasant for everyone.

One of the courses was a 3-day course, so we had to do 4 half days and a final full day. But we did not, I made sure we edged a little further into the material each day than I had planned and, except for one week, I was able to make that last, full day shorter. The odd thing was, even though I did end the material early on Friday, most people stayed around after to discuss a few things or would listen to a slightly off-topic, undemanding, final session. 

A BIG mistake I made on the first course was thinking we could trim the coffee/tea breaks as there were not going to be issues with the loos (well, not ones I could do anything about!) and everyone had their own source of drinks and snacks. It was a “three-day” course and I was trying to get a little ahead so we could shorten the Friday. So we had 5, 10 minute breaks –  bad move. It’s mentally more demanding to take in information via remote training I think, people needed the breaks. If anything, I ended up in later courses giving the delegates longer breaks than we would have a training room. 

4 – Don’t give them Anything!

If I was on a remote training course and I had been sent the materials, I know what I would be tempted to do… Especially if, like is nearly always the case, you have more work to do than you can get done.

I made it very, very clear that they would get all the slides and that there were lots of words to explain the diagrams I tried to mostly talked around. But not until after the course. So they had to listen or goof off. If I’d given them the slides, most of them would have just goofed off!

I mostly sent the course notes at the end of the week but a couple of times I sent them at the end of the day. This was usually as someone was forced to skip a session and they asked for the notes to catch up. I generally take a very dim view of people skipping sessions on a course, I design the course with a flow of information that grows and builds over the days, but we live in weird times. Some people were juggling childcare, relatives, stuff simply going wrong.

On the topic of course materials… Don’t you hate it when bullet points appear on the screen one-by-one? It usually makes for a relatively poor presentation. But when remote training and you want to slow down the rate of information you are delivering or make points clearly, they can come back into their own – IF you don’t over-do it. People are concentrating on the screen way more than in a normal presentation, when you the presenter are a main feature, so the point-by-pointy method is more suitable. (A friend did point me at some software that would overlay my image over my slides so I could “present” as normal, but I would have had to re-jig a lot of slides for that and it was an added complexity I wanted to avoid. Maybe next time).

If you can, concentrate on images and diagrams, especially if you can animate them. Even something simple and cartoon-like gives a bit more, well, animation! More visual stimulus and something you can talk around is better than text. You still have the wordy slides, but they are more for the delegates to refer back to or to quickly remind me of things I need to cover.

5 – Odds & Sods

I kind of touched on this earlier, but up the human, interactive side as much as you can. Banter. I do this in physical course too, but it really helped with the remote sessions when I got it to happen. Someone is usually OK for a bit of mild mickey-taking. If you say something self-derogatory people will often join in and you go from there. I also try and tell a few more anecdotes and they sometimes prompt one of the delegates to reciprocate. The more conversational flow you can generate the more people are willing to both listen and speak up.

Do keep track of the anecdotes, especially if you are running a course multiple times. I do have specific points in the course where an anecdote highlights a point, others are more “on a whim”. I remember being a delegate on a course about 28 years ago and the instructor, a very entertaining chap, told quite a few little stories. I noticed that after doing one he would often make a note or something on his paper pad. I asked him about this at a break and he explained that, as he ran training courses pretty much every week, he lost track of which stories he had told. So he made a little note of each one.

Get the delegates to ask as many questions as you can, almost beg them to – and always been keen to answer them immediately, even if you know you’ll cover the point later in the course. It’s good interaction, encourages more questions to be asked, and there is a reason they asked that question then. If it is something that is not covered later in the course, the next version of the course may well have a new slide on it!

My only exception is if someone asks a question about a part of the course I knew they goofed off from or they were late for the start of. I’ll probably answer the first one or two and make the point we covered this, and then I’ll say we don’t have time. Don’t get me wrong, I’ll answer the same stupid question 3 or 4 times if the person is just not getting it, but I don’t condone people skipping parts of the course by re-iterating what they chose to miss. I give the course to people who want to learn.

Numbers. Have fewer delegates on the course than you would in the flesh. With a web cast, a single presentation at an audience, the more people listening the better. The communication is one way. But a training course is actually nothing like that, not if it is a good course. You need to be able to interact in all the ways I have described, and it is harder to do that remotely, and the whole process is just so much more draining via screens & microphones. I had to really kick back on this one initially and I am glad I did. I had delegates numbers from 4 to 12. When there was more than 8 of them, I had to give up on keeping tabs on all of them and those weeks left me shattered. I can handle 12 in a room no problem, but I think 6-8 is the ideal for a remote, interactive course.

 

 

 

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Finally Getting Broadband – Via 4G! (cable-free, fast-ish internet) February 15, 2021

Posted by mwidlake in Architecture, Hardware, off-topic, Private Life.
Tags: , , ,
2 comments

I live in a field. Well, I live in a house, but it and a few other houses make up a tiny hamlet surrounded by fields. My back garden is itself a small field. It’s nice to live surrounded by countryside, but one of the drawbacks of this rural idyll is our internet connection. Our house is connected to the World Wide Web by a copper telephone line (via a British Telecom service), and it’s not a very good copper telephone line either. I joke that wet, hairy string would be just as useful. Our connection speed is, at best, about 5Mbps download and 0.4Mbps upload. That is not a typo – nought point four megabits a second. My dual ISDN line back in 2003 could just about manage that. At busy times it’s worse – a lot worse – as all the houses in our hamlet contend for whatever bandwidth we have back to civilisation. Evenings & weekends it has almost become a not-service. It is not broadband, it’s narrowband. I pay £23 a month for the wire charge & unlimited calls, another £25 a month for the calls beyond “unlimited” (yeah, tell me) and £30 a month for the narrowband connection. Ouch!

It’s all fields and very little infrastructure…

 

Good BT service.

My neighbours have complained to BT about our internet speed many times over the years and I did also. I was told (and I paraphrase) “you are at the end of a long piece of old copper-wire-based technology and there are not enough people living there for us to care about, so it is not changing”. Which to me utterly sums up my 30 or so years experience of British Telecom, a company I loath with a passion. I asked if I could get a discount for such a shit service and was told I was on their cheapest deal already. “Would I get better service if I paid more?” No. Well, at least they were honest about that.

About 2 years ago a company called Gigaclear came down the road to our little, rural hamlet. They are being paid a lot of money by Essex county council to lay fibre cable to rural locations all over the district. This raised our hopes. Gigaclear dug channels, lay down the ducting, put a green telecommunications box in place by “Joe on the Donkey” (this is the real name of a neighbour’s house) – and went away. They’ve been back a few times since, but the promised super-mega-fast fibre broadband service they touted has not come to fruition. The last two visits have been to check out why they can’t connect anyone. It might partly be that one pair could not even understand that the green box 100 meters away is probably the one that is supposed to service our house, not the one way across two fields that they have not dug a channel from.

 

Bad Weekend BT service

I first realised there was another solution when, forced by evenings & weekends when download speeds dropped to below 1Mbps, I started using my iPhone as a hotspot for my laptop. 5/0.4Mpps was replaced by 15/2.0Mbps. I was soon using my phone to upload pictures to social media and the charity I foster cats for, plus for video conferencing for work & social purposes. If my mobile phone was giving me better connection speed, why in hell was I using an expensive & slower connection from my physical telephone line? One problem was I only have so much download allowance on my mobile phone (10GB). The other was you need to keep the mobile by the computer to tether it. It was not a mobile anymore!

I was then chatting to a neighbour and he said he’d tried a relative’s 4G broadband from EE – EE is about the only phone network we can get a decent signal with here and we use them for our mobile phones – and he was pleasantly surprised at the speed. He said it was expensive though…

As a result of this chat I did a quick check on the EE website. A 4G EE broadband device (basically a box with the electronics for a mobile phone and a router in it) would be cheaper than my current BT solution! £35 a month, no up-front fee, and their advertising blurb claimed 31Mbps on average “in some places”. I had no expectation of getting anything near that sales-pitch speed, but repeated speed test on my EE mobile phone was confirming 15 Mbps download and 2 Mbps upload usually, much better than the BT landline. And the offerings of Gigaclear, should they ever plumb us in, was for 30Mbps for a similar cost to EE 4G broadband, and 100Mbps if you spent more spondoolies. All in all, EE seemed not that expensive really and, as I said, cheaper than sod-all bandwidth with BT!

The last thing I checked was if you could get a physical EE 4G signal booster if your signal was poor. Yes, you can, but from 3rd party companies for about £250-£400. Our EE signal in Widlake Towers is better than any other mobile phone operator but it is never an all-bars signal.

The Change to 4G, cable-free Broadband

I decided it was worth a risk. All I wanted was the speed my iPhone was getting and, if it was poorer, a one-off spend of maybe £300 would help matters. I ordered an EE 4G router and 200GB of data a month. Why so much data? Well, I had never exceeded my 10GB data a month on my mobile phone, I am not what you could call a big data user – I do not download films or live stream stuff. But my connection speed had been so bloody awful for so long I had never even dreamed of downloading 1/2 hour TV programs, let alone whole movies! Maybe I might with a better connection. And I was about to start running training courses for a client. I figured I would bet on the safe side.

My EE 4G router turned up the next day, I was so excited!

It was broken. It would get the 4G signal no trouble but it’s wifi service was unstable, it shut down under load. It was so annoying as for 10 minutes I had FORTY Mbps download and FIFTEEN Mbps upload performance! I count this as mental cruelty, to let me see the sunny uplands of normal 1st world internet access but to then immediately remove it from me…

It was clearly a faulty unit so I was straight on to EE. It took over an hour and a half to contact & talk through the issue with EE but, to be fair, they have a process to go through and they have to make sure the customer is not doing something daft like keeping the router in a basement, and they sent me a replacement unit the very next day.

This is more like it!

It arrived. I plugged it in. It worked. It’s was great! The bandwidth was an order of magnitude better than the old BT router over the fixed telephone cable. Not only that, it also far exceeded both what I had got via my phone and also the estimates of EE. I got over 60Mbps download on average and often above 70 Mbps. The highest I have seen so far is 98Mbps. Upload averages around 14Mpbs and has gone up to 30 Mbps at times – but I have to say I see the peak upload when download is a little depressed. On average I am now getting consistently over 60Mbps download and 10Mbps upload speeds, though sometimes when the local network is busy (mid workday afternoon) I see a little less. “Peak performance” is weekend and evening times, I get fantastic performance, maybe as business users in the area are quieter and few domestic clients are using the 4G network.

So, over 60Mbps download and 10Mbps upload average and sometimes more – I’ll take that! more than 10 times faster download and, well, 30-50 times faster upload then BT over tired copper.

It’s utterly transformed my online experience. I can honestly say that when I see slow internet performance on web pages now I am just as inclined to blame the remote site as my connection. And I can upload pictures & emails in a way I have never been able to before. Until now I was notable to put up short videos of our foster cats to the charity website unless I did it on my phone in the garden, and that was hit-and-miss. Now I can just chuck videos over to them and not worry about it. For me it is a game changer.

My 4G Choice

In the window, catching rays – 4G rays

I had little choice but to go for EE as no other mobile phone company has decent coverage in my area. You may also have only 1 choice but, it you live in an area where many 4G services are available (i.e. you live in a place where other people live!) then look into which is best – not just for speed/cost but also customer service. Many companies are offering wireless 4 and 5G services. Personally I would stick to 4G as 5G is still shiny and new enough to come with a price hike for not-a-lot more total throughput. I’ve always been really pleased with EE customer service. For years I’ve popped over to one of the two local-ish EE shops whenever I have needed to change something or had a problem and they always sort me out quickly. Not only that, on a couple of occasions I’ve suggested I go for a more expensive plan (say to get more roaming data allowance) and they have looked at my historic usages – “Mate, you’ve never been even close to the smaller plan, save yourself £10 a month and take the cheaper one. You can always upgrade”.

I went for EE’s standard 4G Home Router as the only difference I could see with it and their 4G Home Router 2 was the Home Router 2 supported 64 devices not 32, for an extra £50 up front.. Between us Mrs Widlake and I have fewer than 10 devices, let alone over 32…. At the time of writing there is no initial charge for the 4G Home Router, just a £35-£55 monthly charge depending on what data allowance you want £35=100GB, you get an extra 100GB for each additional £5 up to 500GB but then at £55 it becomes unlimited. You can choose between 18 month contract or no contract and an up-front fee, but go look at the website for details, it will have changed by the time you look (I know this as they have introduced a 5G home router between the time I started this blog post an ended it! But I have no 5G signal so of no consideration for me).

In line of sight of the study window

Initially I had the EE 4G home router in the main room of the house so I could fiddle with it if needed, but I soon moved it upstairs to a bedroom where prior tests had shown I got a better 4G signal. (You want as little in the way of building materials and geography between you and the 4G mast, so upstairs by a window is ideal. And in my house the top floor where I put the router is made of wood, straw, mud, & horse shit. Other parts have fully insulated plasterboard which includes a thin metal foil layer to both reflect heat and, unfortunately, block electromagnetic radiation).

Spreading The Network

Another consideration for me was allowing the wifi signal to get to the study. The study is above the garage, a structure covered in black clapperboard which is strangely attached to the neighbour’s house (this is the sort of thing you get with properties hundreds of years old – things just got built). A few years ago when we had the study/garage rebuilt to modern standards we got another company to provide telephone services to the study, to see if it was better than BT. It was. A bit. And it still is. But that company is now part of BT (as is EE to be fair) and is slower than my mobile phone. If the new router reached the study we could stop using BT AND we could stop using this backup supplier (which was cheaper than BT but more limited in some respects). With line-of-sight I hoped the wifi would reach the study. It did  – but it was right at the range limit and the signal would drop :-(. If you moved your laptop or tablet away from the window and clear line-of-site, you lost the Wifi signal from the new 4G broadband router.

I see you (just) router

Well, I had a possible solution to this too.

There are many wifi extenders on the market at many prices, some just use wifi and some use your power cables and others create a mesh. If 30 years in I.T. have taught me anything it is that there is something deficient in my head that means I personally have no affinity for networks. I need simple. I knew I could not use a power cable solution. With these you plug one device in a socket and it communicates over your domestic power lines to a second plugged-in device which provides a wifi service. For historical reasons my study is on a different power circuit to the house, I doubt it would work. I did not want to go to Mesh as I felt (based on experience) I would fuck it up. I just wanted a simple, single WiFi extender.

After a few hours on the internet I came to the conclusion that there was a solution, a relatively old device (first sold in 2016) that might be what I wanted. A TP Link RE450, also known as an AC1750. It was simple and excelled at having a long range. I ordered one for £50 quid.

It came and, following the simple instructions and maybe half an hour of my part-time attention, I had it working and connecting to both the 5 and 2.4 GHz networks of my EE 4G broadband router. I moved the TP Link RE450 over to the study and plugged it in so it had line-of-site to my EE 4G router. The connection light flashed blue and red, which suggested it was not happy – but I worked out that it was happy with the 2.4Ghz connection but not the 5Ghz one. It was right on the edge of it’s range. A bit of fiddling of orientation (hat tip to Mrs W who realised it was better on it’s side) over 2 days, including moving the router a whole 30cm closer, and now both are happy.

The end result is I now have access to the 4G EE broadband router in the study & garage at about 20Mbps download and 12 Mbps upload. I think the limit is the TP Link to EE router connection, which is just down to distance. Bottom line, I now have access to the internet from every part of my house and separate study, and the whole front garden, and the edge of the field opposite the house, and some of the back garden, at speeds substantially faster than my old landline.

British Telecom will be getting a cancellation notice from me by the end of the month (I need to change some email addresses) and the third party service to the study will also be terminated. I will replace a service from BT that was costing me £80 a month and another that was £30 a month with just one at £40 a month, which gives me a much, much better service.

That feels good.

Latest speed test? Done as I completed this post, I recorded 77Mbps download & 30Mbps upload, which I am incredibly pleased with. I don’t expect to get that all the time though.

Speed test the morning I posted this. It will do 🙂

 

Sourdough – Making a Loaf January 19, 2021

Posted by mwidlake in Baking, off-topic, Private Life.
Tags: , ,
4 comments

<<– Creating the Sourdough Starter

Nothing beats fresh, home made bread

Anyone who follows me on Twitter knows I like making sourdough bread. For me, a sourdough loaf is a real treat. I love the combination of a thick, crunchy crust and the soft, strong-flavoured inside. I’ve been asked a few times how I make my bread and I keep saying I will write it up. This blog post is the fulfilment of that promise.

Making sourdough is a longer, more complex baking process than most modern versions of baking bread, but it is actually a very old method of baking and was probably the main method used by the peasant and working classes over the last few hundred years. It takes several hours to make sourdough. I start mine in the evening and bake it in the morning.

Work is stressful (even working in I.T. from home), this pandemic is stressful, baking a nice loaf of bread helps balance that stress.

A key part of the process is that you need a “starter”, a mixture of flour, water, and actively growing yeast. I did a long and detailed post on creating a starter about a month or so ago. If you created a starter then and have been feeding it since, it’s well past time to make a loaf!

Get the Starter Active

If the starter mixture is in the fridge, take it out of the fridge several hours before you are going to use it. If I am making my dough in the evening (my usual method so it can prove overnight) I take the starter out the fridge about noon.

A few hours before you are going to make your dough (usually 6 hours or so for me), mix up 200 grams of strong, white bread flour with tepid water so it is a similar consistency to porridge, add it to the starter and give it a good stir.

This should help get the starter really active and, after a couple of hours, you should see bubbles in the mixture and the volume will increase. I do not seal the jar during this process, I leave it with the lid over the top of the jar but not clipped or screwed down.

Making the Initial Dough

I’ll give you two recipes for making the dough. The first is from a man called Paul Hollywood, who is a very well known and successful baker in the UK. He is one of the judges on “The Great British Bake off“, which is one of the most popular TV programs in the UK. I know the program has been syndicated across the globe, with over 25 countries showing their own version, and a couple showing the UK original. The second recipe is mine, which is derived from Paul Hollywood’s. I increased the size of the loaf as I wanted something to provide sandwiches for 2 people for 2 days and I found a little more salt and a lower percentage of starter gave results I preferred. Less starter seems to give a better final rise to the loaf. Please note – Paul Hollywood is a considerably better baker than I! Perhaps try his recipe first.

This Kenwood Chef is 40 years old!

Paul Hollywood recipe

  • 375g Strong white bread flour
  • 250g sourdough starter
  • 7g salt
  • 130-175 ml tepid water
  • a teaspoon of olive oil

Martin Widlake recipe

  • 500g strong white bread flour
  • 200g sourdough starter
  • 10g salt (but no more!)
  • 7g sugar
  • 200-220ml tepid water
  • a teaspoon of olive oil

 

 

The below is based on my recipe

I have a little plastic jug for measuring the water. Before I put any water in it I put the 10 grams of normal, fine table salt (1). Do not go above 10g of salt in 700g total flour & starter as too much salt inhibits the rise of the loaf. I’m adding about as much salt as you can without this happening.  I also add a teaspoon of sugar (7 grams) as I feel it balances the sour of the loaf and slightly boosts the loaf flavour. Skip this if you like.

I then put 500 grams of strong bread flour into the mixer bowl (see later for some variations to 500g of flour). As I add the flour I also dribble in the salt/sugar mix. This is to help it all mix in evenly. I found that if I just chucked the salt in after all the flour, again the rise could be problematic and the bread seemed to be a bit patchy in it’s flavour. Give the flour with the salt/sugar in a quick swirl with a spoon or something.

I now add 200 grams of sourdough mixture and about 100ml of the tepid water. I do not add it all as I use a food mixer to initially combine my dough. We have a Kenwood Chef that is 40+ years old. To make bread dough in a food mixer you need a dough hook. The one you see in the picture by the recipes is only a few years old, it is coated with Teflon to help the dough to not stick to it.

The mixer can throw little fountains of dry ingredients out of the bowl so I put a towe over the whole thing. If you do this, make absolutely sure the towel is not going to get caught on the dough hook/mixer! With the mixer on it’s lowest setting, I slowly add more of the water to each side of the bowl so that the ingredients combine. I have found that as the dough mixture gets towards the consistency I want, or is damper than I am aiming for, it wraps around the dough hook and no longer mixes! It just wizzes around with the hook.  This is why I added the water slowly and keep about 20-30ml in reserve. Then, when all the ingredients are well mixed but it is not quite forming a single ball, I add the last of the water and keep the mixer running until the dough does wrap around the hook and stay on it. Take it off the hook and make it into a rough ball, as shown In the picture of the mixer.

You can mix it all by hand, which is fun, but your hands get really messy and it takes longer. If you do mix it all by hand, add the water bit by bit until the dough is quite sticky.

I now put a little olive oil, half a teaspoon is all, on a thoroughly cleaned work surface and spread it around  into a 20-30cm circle. I drop the dough in the centre of this and I knead it by hand to finish it off and get a smooth consistency in the dough. Different people like to mix their dough in different ways. I push into it with the heel of my hand, stretching it against the work surface, and then fold it over a little and push into it again. I do this with just the one hand in a regular rhythm of about one one push a second, slowly rotating the dough ball and moving it around so I am working all of the ball. I swap hands occasionally for a full upper-body workout…

Other people slap the dough onto the work surface or throw it down, others squidge it out with both hands and then fold-and-squidge. Do what seems right to you. There are lots of videos on the internet.

The whole aim is to get all the ingredients mixed in smoothly and keep going until the dough is a little elastic. Apparently the best test as to whether you have worked the dough enough is that you can stretch some thin with your fingers and see light coming through it. I don’t do this, it does not seem to work well with my dough, maybe as I do not add enough liquid, maybe because sourdough is a little different. I know it is ready as it…. feels ready. Smooth, not rubbery, but with some stretch to it. Because I use a machine to initially mix and knead the dough I only have to hand knead it for 5 minutes. If you mix the dough by hand then you will need to knead it for 10, 15 minutes. Maybe more.

The whole idea of the kneading is to get some of the protein in the mix, the gluten, to form long chains which give the final loaf it’s structure of a soft and flexible material. If you over knead the dough then the bread will not rise so well and the bread will be rubbery and dense. You don’t want rubbery, dense bread.

Grow my little beauty

Proving the Dough

Once your bread is kneaded to the consistency you want, you have to let it prove – which means left alone to grow. You prove the dough twice.

Use the other half a teaspoon of oil to lightly oil the inside of the mixing bowl. The only reason for the oil is to stop the dough sticking. Put the dough ball into the bowl and cover with clingfilm or similar. I use a clear, plastic shower cap that I can re-use dozens of times as (a) it’s so easy to pop it over the bowl and (b) less plastic waste.

You need to keep the dough at about room temperature – between 18C and 22C – for several hours. Less time if it is warmer, more time if it is cooler. I make my dough about 8-10pm in the evening and leave it overnight, near a radiator that will come on in the morning. This seems to work for my dough.

During the proving stage the yeast in the dough consumes sugars (the sugars come from the starch in the flour being broken down) and they produce carbon dioxide (CO2). this is what makes the dough grow and become soft.

In this first prove of the dough it should doubled to tripled in volume, and become soft and spongey to a light touch. Sticking a finger in it will leave a dent that only partly fills in.

Lightly dust a clean, dry area on your work surface with plain or bread flour and turn the dough out of the bowl it has proved in onto the area. I lightly dust one side of the bowl to stop the dough sticking to it and I ease the dough from the sides and bottom of the bowl with a small, flexible spatula – one of those made of silicon or soft, heat resistant plastic. In the picture above of the dough on the work surface you can see bubbles in it – this is from the CO2.

 

Knocked-back dough ready to go into the banneton

You now need to “knock back” the dough – knead  it all over with your knuckles or, like I do, give it 30 seconds of kneading like you did when you first made the dough. Some instructions tell you to do things like make a ball after knocking it back and  tuck the dough down under the ball and into the bottom of it. I think these are to create little air pockets in the dough that make the large voids you get in posh hippster café sourdough. I don’t want those large voids. I keep the flour dusting to a minimum and push the dough together well to avoid any air gaps or having any folds in the dough which do not “heal” (stick to each other).

Push the dough down into the container

A nicely second-proved dough

You now need to let the dough prove for a second time. I use a “banneton” for this, a special wicker or similar material bowl that is specifically for the final proving of bread. They also impart a nice pattern on the loaf. Dust whatever bowl or banneton you are using well, put the dough into it and push it down firmly. Lightly dust the top and then cover a plastic bag or similar. You want the bag to be above the dough so when it rises it does not contact the bag, as it will stick to it.  I put the showercap I used earlier back over it, with the damp side inwards to stop the top of the bread drying out too much. Put somewhere warm and leave for two hours. If the house is not that warm, I put the oven on and set it to 50C, then turn it off and pop the loaf in that. If you are dead posh you might find your oven has a proving oven compartment or a plate warmer you can use.

After a couple of hours the dough should have risen a little again and have a smooth top. It is now ready to bake

Baking the Bread.

Ready to bake….

A key to getting a good bake where the bread rises evenly and you get a good, strong crust is moisture. You need the atmosphere around the loaf to be damp for the first 20 minutes or so of baking.

I’ve achieved this with two methods – baking in the oven with a tray of water, and using a Dutch Oven.

In the Oven With a Tray of Water.

Pre-heat the oven to 220C and put a shallow tray on the lower shelf.

Heavily dust a baking tray with flour, or flour and semolina (semolina is better at preventing the loaf from sticking, but I find flour on it’s own works just fine and I stopped using the semolina as I’m lazy). Carefully tip the loaf out on the tray and slash the top several times. I have a special, small, gentle serrated knife just for this, it seems to work better than a smooth blade. He’s called Mr Slashy the knife. This scouring allows the crust to expand more easily during the cooking.

 

… but it did not go to plan

Dust lightly with flour and immediately put the loaf into the oven, and put about 500ml of warm water in the shallow tray. This will create steam as the bread cooks.

Cook at 220C for 30 minutes and then turn the oven down to 200C and cook for a further 15-20 minutes. The bread should have risen and turned a lovely golden brown. You can test if it is done by tapping the bottom of the loaf, it should sound hollow. If, like me, you like your bread slightly darker with a stronger crust, extend the higher temperature period from 30 minutes to 35, 40 minutes.

Take the loaf out and move it onto a wire rack to cool.

In the example I show, the loaf is a weird shape. I think this is because, with this loaf, I forgot to put the water in the oven with the loaf, then added cold water to the tray, not warm. As a result there was not enough moisture, the crust formed early and the still-expanding loaf could no longer grow and burst out the side of the crust. If this happens to a lot of your loaves, try scoring more or gently wetting the top and sides of the loaf before the final dust of flour.

It tasted just fine!

In a Dutch Oven.

A Dutch oven is basically a heavy iron or aluminium casserole with a well fitting lid. You bake the bread with the lid on initially to trap moisture. I use an iron casserole dish about 26cm in diameter. The casserole needs to be about 5cm wider than your uncooked loaf, to allow for expansion. If you already have a casserole dish you might need to change your loaf size or the bowl/banneton you prove it in so that the loaf fits!

Pre-heat the oven and the casserole dish to 230C. Yes, 230C. It take about 15 minutes for my casserole to heat up fully.

Take out the casserole and  heavily dust the bottom with flour. You will know it is warm enough as the flour will smoke gently.

As carefully as you can, turn out the loaf into the casserole dish. I turn the banneton upside down and hold the loaf in place with my fingers, shake it slightly until the loaf drops onto my fingers and then I open my fingers to let it drop the 6 inches into the casserole. Do not let your skin touch the casserole dish, it hurts like hell! Slash the top of the loaf several times, again keeping the fingers away from the hot metal.

Take the lid off at 20 minutes

This is the main disadvantage of using a casserole, getting the loaf in and slashing the top is harder and the danger of a nasty burn is ever-present. I have tried turning the loaf out, slashing it and then transferring it to the casserole, but it knocked a fair bit of air out the loaf and reduced the rise.

Cook at 230C for 20 minutes. Remove the lid (the loaf will still be a cream colour) and cook for a further 15-20 mins. Turn the oven down to 160 and cook for a further 15-20 mins. You turn the temperature down more with the casserole as it retains heat for a while.

You might notice my oven says 235 and 165C. My oven temperature is a little cool (I tested with an oven thermometer) so I added 5C. You do get to know your oven when you do baking!

 

 

 

 

 

After 20+15 mins on high, turn down

You loaf should now be dark golden brown. Remove the casserole from the oven. I put a little fan blowing air over the casserole for 5 minutes before I extract the loaf. Using a cloth to protect your fingers, take out the loaf and leave to cool on an a wire rack.

I swapped to the Dutch Oven method as a couple of friends recommended it and the flush of steam from the “oven with a tray” method was making the control panel of my oven go funny. I’ve already had it repaired once.

Having swapped, I think overall the Dutch Oven method gives a better loaf. I have far fewer issues with the loaf rise being uneven and part of the load bursting out the side or the crust “tearing” at the sides.

If I decide to make larger loaves I’ll simply swap to the oven-and-a-tray-of-water method.

 

 

 

Cooling

Once the loaf is out the oven I tend to start losing control of my salivary glands and I am desperate to eat it, so I use a little fan to help it cool in about 1/2 an hour. If you have more will power than I then it takes an hour or so for the loaf to cool naturally.

I love to cut open the loaf and eat it when it is still a little warm. The one disadvantage of this is that the loaf will lose extra moisture as a result of this, so any bread you save until tomorrow will be a little drier. I hardly ever manage to hold off cutting it early for the sake of a better experience tomorrow!

Notice the lack of large voids – perfect for sandwiches

Alterations to the recipe

I sometimes replace 150-200 grams of the white bread flour with spelt or mixed seed flour. It does seem to drop the rise a little though. I have tried adding a little dried bakers yeast to balance this but with limited success.

I have replaced all 500 grams of white bread flour with brown bread flour. It was OK, but despite me generally preferring brown bread,  with sourdough it just does not seem right to me.

I really like adding a teaspoon of smoked, sweet paprika to the mix. This is partly why I put the salt etc in the jug I later user for the water, I put the extra flavour in the jug too and the water washes out any flavouring that has remained in the jug.

Chop up a handful of sundried tomatoes (drained of their oil on kitchen paper as the oil seems to inhibit the rise) and add those with a good squirt (say 25ml) of double strength tomato puree.

 

1) You could use sea salt or Pink Himalayan salt instead of dirt-cheap table salt –  but it’s all the same stuff really, it’s dried out sea and mostly consists of the specific salt compound sodium chloride. The stuff dug out the ground is from a few hundred million years ago and sea salt is usually from drying out current sea water. The problem with salt that is not table salt is it is probably not as fine so it might impede rise more.

 

Covid-19: A Primer On DNA, RNA, and SARS-CoV-2 January 13, 2021

Posted by mwidlake in biology, COVID-19, science.
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I want to explain a few things about SARS-CoV-2 (the virus that causes Covid-19) and the vaccines that are being rolled out in both the UK and the world. To do so I first need to explain about DNA, RNA, proteins and what is called the central dogma of molecular biology, which is what this post is about. The central dogma is the core – the absolute fundamental key thing of life, of our biology. It is the biological equivalent of what quantum mechanics is to physics.

Thankfully, it is far simpler to understand the basics of the central dogma of molecular biology than the basics of quantum mechanics. It is also a well established concept, I was taught it last century at university and it has not changed much in the 32 years or so, though we better understand so much more of the details and ramifications now (6).

Central Dogma Of Molecular Biology

Basically the Central Dogma is that DNA makes RNA and RNA makes protein – and information does not flow backwards. I’ll try and explain that in steps, but before that I want to give a quick reminder about DNA, which most of you probably remember from school, and protein/polypeptides. Sorry, but it’s necessary. Skip to “The Core Of Biology” if you already know all about these.

DNA and Proteins

DNA molecule – from Yourgenome.org

All living organism contain and are controlled by DNA – Deoxyribonucleic Acid. This is the helical, double-stranded molecule whose structure was worked out by Watson, Crick, and Rosalind Franklin. In all organisms (except bacteria & archaea – together known as prokaryotes) the DNA is held in the nucleus of the cell (1). The whole genome is in every normal cell in an organism (be it a plant, fungus, moss, animal, you. Everything alive that is not bacteria/archaea is a eukaryote – which means the cell has a nucleus). There are some exceptions – such as red blood cells that lack a nucleus, or sex cells that carry one half of the normal amount of DNA for a given species.

The DNA directs all of the biochemistry of an organism (2). Everything. It defines the structure of the proteins we are made of, how the proteins go together, the layers and parts of our organs, the overall plan of our bodies, and the hormones, chemicals, and free-moving cells that go around our bodies like red and white blood cells. We still don’t know how some of this control is done but as DNA changes (mutations) affect all of these things, we know the DNA is basically the instruction book to both make an organism and to keep it functioning.

The DNA of an organism contains (amongst other things) it’s genes. Genes are the instructions for making all of our proteins and we say the genes are “expressed” when the genes are activated and make the proteins. And they do this all the time, at great rates, churning out vast quantities of proteins in each and every cell.

I say proteins but that is not *quite* right. Proteins are made of polypeptides, and polypeptides are made up of amino acids. As an analogy, proteins are paragraphs, polypeptides are sentences, sentences are made of letters which are the amino acids.

In the vast majority of organisms there are 20 different amino acids available to “spell out” all polypeptides. Genes have instructions to make chains of amino acids, called polypeptides. A protein may be a polypeptide, but it might also be made of several polypeptides or polypeptides that have been chemically modified after being initially made. I make this point as below, and in some of the links, polypeptides and amino acids are referenced and general scientific literature can be a bit muddled between polypeptides and proteins. For now, just think of proteins as really complex polypeptides. (3)

DNA consists of four letters as you probably know. Adenine, Cytosine, Guanine, and Thymine. In the double helix the two strands are “inverse mirror images” of each other and the letters pair up – A with T and C with G. So a short strand of DNA might be something like the below and, as indicated, the two halves can be split and, via the pairing of the letters, perfectly copied:

Double stranded DNA can be split and (perfectly) duplicated

The DNA is unzipped and split (by an enzyme called Helicase) and then DNA Polymerase can come along and add in the missing letters and you end up with two perfect copies. Usually. In my example, to the right, there is a mistake,  – a C has been added in where an A should be. This mistake is an example of a mutation.

However, that is not part of the Central Dogma. Although DNA duplication is vital (after all, every cell needs a full copy of the organism’s genome so the DNA needs to be replicated each time the cell divides). The main function of DNA is to pour out instructions for the creation of polypeptides

Central Dogma by Brownfield 5 on slideshare

The Core of all Biology

All the complexity of what our cells do and how our biochemistry works is via genes being expressed.  I’m not going to even attempt to describe how gene expression is controlled. It’s incredibly complex, it’s an area of understanding that has advanced hugely since I was taught the basics in my degree 32 years ago, and science still does not really understand a lot of it. But it’s the expression of these genes that allow are cells to do what they do, from growing hair, muscles, and making white blood cells to producing the enzymes that digest our food and control our bodies. All cells express thousands of genes all the time, at different levels of expression, and they do this by producing Messenger RNA, known simply as mRNA.

RNA, or Ribonucleic Acid, is (as the name implies) structurally very similar to DNA. It is single stranded, not double stranded like our genomic DNA, and the Thymine is replaced with a very similar chemical called Uracil.

Transcription

When a gene is expressed the relevant piece of DNA is “unzipped” and an enzyme called RNA Polymerase walks along the DNA and creates a complementary (meaning A becomes U, T become A, C becomes G and G becomes C) RNA copy of the DNA, as is shown in the diagram to the right. This is called transcription and it produces something called pre-mRNA. This is itself then processed by by other enzymes which cut out parts of the RNA that represent “Introns” – bits of DNA in the gene that are not to be used. This bit is not shown on the diagram. It is one of the complexities of our DNA that was poorly understood before the Human Genome Project and is still rarely explained. In a complex organism like a mammal or plant or fish, a single gene can produce a range of proteins depending on how this pre-mRNA is processed.

The diagram below shows how the double-stranded DNA is “unzipped” and the RNA polymerase reads one strand of the DNA and produces an RNA strand based on it.

RNA Polymerase, from BC Opentextbooks

The final mRNA consists of three main parts. The first part, at what is called the 5 prime (or 5′) end is a cap that allows the mRNA to be recognised and grabbed by the Ribosomes (see later) and transcribed. Then comes the RNA equivalent of the DNA gene for the protein. At the other end, the 3 prime (or 3′) end, a string of As is added (100-200 of them normally), the poly-A tail. We will see why later.

Pre-mRNA to mRNA from Wikipedia

This mature mRNA is then transported out of the nucleus of the cell and out into the body of the cell, into the cytoplasm. The mRNA may hold markers to say where specifically in the cell it is to go but that’s a detail I won’t go into. This seems to be very important to complex organisms like ourselves, that the DNA sits in the nucleus, mRNA is produced and this is quickly passed out of the nucleus to be processed elsewhere in the cell.

Translation

So we now have an mRNA molecule in the cell ready to be translated, i.e. used to make a polypeptide. In the cell there are thousands and thousands of very complex molecules called “Ribosomes”. A ribosome is actually made of two parts, both of which are themselves made out of RNA, not protein. These ribosomes clamp onto the cap of the mRNA, one part on one side, the other on the opposite side, the mRNA in the middle. The cap is a special starter molecule and the first part of the mRNA, which does not code for a polypeptide but controls how easily the Ribosome attaches to the mRNA. The attached ribosome will then “read” the mRNA, working down the string of letters and creating a polypeptide that is described by the RNA sequence.

Special intermediate molecules are used to translate the RNA to an amino acid. These are the tRNA molecules shown in the diagram below. As a ribosome walks along the mRNA is reads small chunks of the mRNA, finds a tRNA that complements the mRNA and temporarily binds it to the mRNA. At the other end of the tRNA is a specific amino acid and this bonds to the growing polypeptide/protein.

Ribosome translating mRNA – from sites.google.com

Many ribosomes can be walking along a single mRNA molecule  at a time, creating more than one copy of the polypeptide. When a Ribosome gets to the end of the mRNA, to the poly-a tail, it drops off (4) and it will (or at least may) snip off the very end of the poly-a tail. So it shortens the tail. This tail protects the mRNA molecule from being destroyed by the cell so, as it shortens then the mRNA becomes more likely to be destroyed. Why is this important? Well, the cell needs to produce different polypeptides at different concentrations at different times. The poly-a tail is a key part of how the cell controls how long an mRNA molecule last for, creating polypeptides. The longer the tail, the longer the mRNA lasts. The mRNA can’t be allowed to hang about in the cell producing polypeptide for ever. Once it’s tail is gone it is destroyed. Thus for a polypeptide to be constantly produced, the genes in the nucleus need to keep producing the mRNA for it.

As you can appreciate, changes to the 5′ cap can change how quickly (and often) a ribosome latches onto an mRNA molecule, the length of the poly-a tail can control how long the mRNA lasts and so how much polypeptide that one mRNA molecule creates, and the nucleus has overall control over when and how much mRNA is produced. These processes allow constant control and change to how a particular gene is expressed.

I’ve said about the RNA being read and converted into a polypeptide. How does this work? The diagram above and the tRNA give clues to this.

How Codons translate to amino acids

As I said earlier, there are four letters of the RNA alphabet – A,C,G, and U – and a polypeptide is like a sentence. There are 20 types of amino acids that are strung together to make our polypeptides. Our genes are written in sets of 3 letters, called codons. You can think of them as a gene “word”. You can see this with the tRNA molecules in the diagram, at one end they have three RNA letters, and the other end the specific amino acid that those three RNA letters translate to.

A codon, such as UCA, codes for an amino acid called serine (or Ser). GCU codes for alanine (Ala). With 4 letters and a “word” being 3 letters long, there are 64 combinations of A,C,G, & U possible. You can see all 64 of these combinations in the table to the left. So how do the 64 possible codons map to 20 amino acids? Well, some codons have a special meaning.

3 – UAA, UAG, & UGA – are stop codons. They mean “this polypeptide is finished, ribosome stop reading”. One codon is special, AUG. This either means “start reading here” (note, there have to be other sequences in the RNA near it to make it mean this) or amino acid methionine (Met).

As for the others, well several codons mean the same amino acid, as you can see in the table to the left (5). Generally the first two letter in the codon define which amino acid the codon is for (anything starting GU is for valine, Val) but for some the third letter is the deciding factor.

Ribosomes thus start at a special AUG codon on the mRNA and then read three letters at a time and for each one, for each codon, the specific amino acid is added to the growing chain – via the tRNA molecules. The chain can be thousands of amino acids long or just a handful. The chain grows until a stop codon is reached. The longest polypeptide is titin, which is between 27,000-35,000 amino acids long (due to those “introns” I mentioned, sometimes some are cut out, sometimes not) and makes muscle elastic.

That’s it. That is how our DNA, our genes, make all the things that build and control our bodies. Of course, there is an incredible amount of complexity that arises from that central process, like how do the proteins control the inclusion of calcium to make our bones, grab iron and put it in our blood, and stuff all that fat in our cells. But it is all controlled and mediated through polypeptides, through proteins and enzymes.

If you want to see a large version of the Central Dogma diagram you can click here:

->ci350poster-141201170705-conversion-gate02

mRNA vaccines.

I won’t go into too many details here, but you may know that a couple of the Covid-19 vaccines are mRNA based. These vaccines are millions of mRNA molecules packaged up into little balls of fat (also called lipid). These mRNA molecules are all the same and are the instructions to produce the spike protein of Covid-19, the bit the virus uses to attach our cells and that the immune system is good at identifying and attacks. This is the Moderna and Pfizer vaccines

The vaccines are ONLY for the spike protein, not the rest of the virus, so the vaccines cannot give you Covid-19. But what the mRNA does do is get into your cells and your cell ribosomes latch on to the mRNA and make the spike protein. The mRNA molecules is not exactly like the one produced by the virus, it is modified to be more stable and last in the cell longer, with for example a longer poly-A tail. The longer it last, the more spike protein is produced. The vaccine mRNA is engineered to produce as much spike protein as possible.

Your body sees this spike protein, it knows it is “foreign” to your body and learns to attack it. Then, if you are infected by the real virus, your body will already know to attack the spike protein and either you do not get ill or you get less ill. Fantastic, isn’t it? I love science and I especially love biology and medicine. Even just 50 years ago this virus would have had to run it’s natural course through us and kill maybe like Spanish ‘flu did, but now we understand so much better what is going on and we can now do something about it. I say “we”, I mean biomedical scientists.

Previous vaccines have relied on getting a modified or damaged version of the whole virus into your body, or modifying another virus that is harmless so that it produces mRNA for exact copies of parts of the dangerous virus. These are hard things to do. The Oxford vaccine is a modified virus (a chimpanzee adenovirus, chosen I believe because it can infect us but does no harm and does not spread in humans).

Advances in handling mRNA, creating it, and understanding how to make it work in our cells, have allowed scientists to create mRNA vaccines which are simpler, more efficient, easy to create or modify , and more targeted than traditional vaccines. Only part of the virus is made and nothing else, so there is no danger whatsoever of the vaccine causing the disease, or a modified version of the disease. Further, if the virus alters (something that is a current worry) then modifying an mRNA vaccine is theoretically very easy and quick. Testing the new version would be necessary and would take months (regulatory bodies allowing – they might let a modified version be fast-tracked, my wife is an expert in pharmacovigilance and she thinks it could be done) , but it means mutations to SARS-CoV-2 can be handled relatively quickly if the need arises. This could be vitally important.

This work has not all been done since Covid-19 appeared about a year ago, it is based on several years of work on MERS, SARS and other viruses. So on the one hand these mRNA vaccines are a new technology, but they are new since 4 or 5 years ago and great advances in how to create them have been made in the last year.

Implications of the Central Dogma

Some things follow on from the above that are fundamental to SARS-CoV-2 and vaccines. I’ll touch on them here and expand on them in further posts, as this is a lot in one go.

Mutations and Open Reading Frame

In my previous post on the new variant of SARS-CoV-2 I mention mutations. At the start of this post I mentioned the copying of DNA/RNA and how mistakes can be made, in particular a single letter changing to another. When a single letter of the genome gets changed, this is called a Single Nucleotide Polymorphism or SNP. If that letter is the first one in a codon in a gene, it is almost certainly going to have an impact. It will change the amino acid inserted at that point in the polypeptide. If you look at the codon table earlier it is possible to change the first letter A to C and still get Arginine. Other than that, altering that first letter in the codon alters the polypeptide. Other SNPs can have no effect – changing GUU to GUC still makes valine. Of course, any SNP that creates a stop codon is going to have a potentially massive effect.

SNPs that cause no change to the polypeptide are called synonymous. As they make no difference to the organism, they occur and get passed to the next generation of the organism and all their offspring. We can use these synonymous SNPs to track the lineage of organisms and they are used to track the lineage of SARS-CoV-2. This allows us to, for example, track how the virus has spread geographically. I say us, I mean phylogenetic scientists.

Those SNPs that change the polypeptide sequence are more likely to change something about the biology of the organism. If the change is negative (for example it reduces the efficiency of an enzyme) the organism and it’s descendants will be at a disadvantage and the change will be selected out. If it gives the organism an advantage, it and it’s descendants will do better than those without the change and will take over in the population. This is true of the new variant B.1.1.7 – is better at spreading, it is taking over. Many SNPs that change one amino acid have very little positive or negative effect on the virus. (I don’t know what it is like on modern genetics degree courses but in my day lecturers would almost come to blows over how much effect a single mutation would need to have to be significant, and how much evolution of DNA was just mathematical, accidental drift, and how much was through selection pressure.)

Other, rarer mutations can be deletions and insertions. Extra letters get added or removed. Now, if the number of letters added/removed is 1, 2, 4, 5 or any number that is not divisible by 3, the impact is huge. Why? Well, a gene has something called it’s Open Reading Frame. Codons are always 3 letter long, staring at the ALU that initiates the mRNA being read. That reading frame of 3 letters per word has to be preserved through the whole gene. If you shift all the letters along by anything other than a multiple of 3, everything after that change becomes very different – and usually garbage.

An insertion or deletion of a non-multiple of 3 letters will not be significant if it occurs in DNA/RNA that does not code for something, but if it is in a gene it is 99.9837% (2) of the time a disaster for that gene, destroying the function of that polypeptide it producers. SARS-Cov-2 is an RNA virus and such viruses are almost all functional gene. Thus deletions or insertions that do not preserve the reading frame are rare (but do occur) in SARS-Cov-2 and other viruses.

Variant B.1.1.7 has 3 deletion mutations in it but they all preserve the reading frame. They drop 1,2, or 3 amino acids out of the polypeptides they code for. But the rest of the polypeptide is preserved. One particular deletion, in the spike protein removing amino acids 69 and 70, stops one of the standard PCR tests from detecting RNA fragments of SARS-CoV-2. I’ll revisit this topic in another post, but because it stops one of the standard PCR tests from working, that can be used in many situations for tracking this variant. Don’t worry, PCR tests for SARS-CoV-2 use 2 or 3 RNA sites to identify the virus, so it is still detected. However, the failure of one of the “channels” has turned out to be a boon for tracking this nasty variant.

Single Direction Of Information.

Under the central dogma you will see that information flows from DNA in the cell nucleus, to mRNA that leaves the nucleus and goes into the cell cytoplasm, and this is translated into polypeptides. It does not go the other way.

Nothing I know of in biology can take a polypeptide, let alone a mature protein, and generate RNA from it. Nothing. Humans can make a stab at it, we can look at the amino acid sequence of a protein and design an mRNA strand that might sort-of work but it’s hellishly difficult as organisms like terrestrial plants and vertebrates have complex post-processing of many polypeptides. Biology cannot do it.

There is nothing that takes mRNA and pulls it back into the cell nucleus and shoves it into our DNA. Nothing natural can do this that I am aware of. A couple of people on a social media forum full of biology experts that I mentioned this post on have voiced possibilities, but nothing concrete yet has been forthcoming (and it would be fascinating to learn about if they do, I’m always looking to learn).

Some of you may have heard of retroviruses such as HIV (the virus that causes AIDS). They can do something that sounds similar – but it is not. They can reverse transcribe their own RNA, i.e. create a DNA copy of their RNA using a reverse transcriptase enzyme, and insert it into the host DNA using an integrase enzyme. The retrovirus has the RNA genes for these two proteins in it’s genome, it brings it’s tools with it. They get into the nucleus of the host cell and use their own tools to insert their own genome into the host, along with control DNA so that the viral DNA can be expressed. What it does NOT do (as far as I know and this is possible where I am wrong) is grab random mRNA from around it and insert it into the DNA of the host. Remember, mRNA is exported out of the nucleus. It’s not there in the nucleus, at least not for long. Also, even if a retrovirus was to insert mRNA into the host’s DNA, it would be doing so without promoter sequences and all the stuff needed to get a gene to be expressed.

I make this point as some people on social media have claimed the mRNA in Covid-19 vaccines could get into your DNA. No, it can’t. It won’t. Anyone claiming this does happen does not understand the central dogma of molecular biology. Either that or they could be in line for a Nobel Prize in biology.

Firstly, the vaccine does not get into the nucleus. Second, there is no biological process native to vertebrates to do the insertion of mRNA into DNA. Third, even if by some chance a virus like HIV was present, and by some miracle some of that mRNA for the vaccine got into the nucleus, HIV is inserting a copy it’s own DNA, not random mRNA hanging around. Finally, even if a miracle on a miracle occurred and the mRNA from the vaccine was inserted into your DNA – there would be nothing to cause it to be expressed. It would just sit there doing absolutely nothing.

What Retroviruses can do is insert into a DNA genome, then when it is expressed it can occasionally pick up DNA from around where it inserted into the genome, which is transcribed and included into the RNA for the virus. If this modified virus then infects another organism and takes that original host DNA (as an RNA copy) with it, it can then insert that picked-up DNA into the new host. It’s very rare, it can happen. But no reverse reading of mRNA was involved.

Basically, the idea of mRNA from a vaccine getting into your genome is damned close to impossible given the current understanding of molecular biology.

Viruses

I’ll finish with some information on viruses.

Viruses are weird. There is an ongoing debate (and has been for over 35 years, as it was a topic of discussion during my degree) whether viruses are alive. Viruses can’t do anything without a cell and it’s machinery to make proteins from DNA/RNA. They can’t move themselves, they get moved about by mechanical processes (in droplets of liquid, floating in water, blown around in the air, transferred via fluids in real living things…). They don’t grow, they do not respond to stimuli (all other life from bacteria up do). They do nothing. A virus consists of just a few things:

  • A string of genetic material, either double stranded DNA similar to what is in us, single stranded DNA or RNA (usually single stranded but occasionally double stranded). SARS-CoV-2 is a single stranded RNA virus.
  • A protein coat, called a capsid, encapsulating the genetic material, keeping it protected and whole. This might be a simple, uniform coat or something more complex made of many proteins. SARS-CoV-2 has a capsid made of several proteins including the famous “spike” protein, which sticks out of the capsid and is what latches onto the ACE2 proteins on our cell walls and allows the virus to get into the host cell.  In SARS-CoV-2 these proteins are embedded in a lipid bilayer (a 2-molecule wide sphere of fat molecules). This is why simple soap is so effective at destroying the virus – it breaks up the lipid bilayer.
  • Protein(s) within the capsid, binding to and protecting the genetic material. SARS-CoV-2 has this.
  • A virus may have an outer lipid (fat) layer, usually derived from the lipid layer of the host cell it infected. SARS-CoV-2 does not have this. {and I might have slightly misunderstood whether this is an extra layer over and above the lipid bilayer that the protein coat can incorportate)

I think of viruses as very, very complex poisons and not alive. Others think of it as alive.

If you want to know more about the structure of SARS-CoV-2 this paper on the structure of the virus on the NCBI site is very good but quite technical.

The genetic material for a standard virus (like SARS-Cov-2) codes for a load of mRNAs that usurp the polypeptide making machinery of the host cells. i.e., they use the second half of the central dogma. Once the virus gets into a host cell, the mRNA is released and it hijacks our own cell’s ribosomes. It makes new proteins to make the virus shell and proteins to coat the RNA of the virus. It creates an RNA Polymerase enzyme to replicate it’s own genetic code and, in the case of coronaviruses like SARS-CoV-2 (and other types of virus) it produces a “checking enzyme” to make sure the RNA copies accurately.

This last point is very interesting. All organisms mutate but RNA viruses are the fastest mutating thing we know of. But SARS-CoV-2 mutates slowly for an RNA virus as it has a check enzyme. That’s one thing to be very thankful for. Influenza is an RNA virus that does not have a checking enzyme, which is part of why it changes so quickly and we need a new vaccine for it each year.

All these bits of the virus then self-assemble into thousands of new copies of the virus, burst the host cell and go and infect other cells in the organism. Some are ejected from the host organism in droplets coughed out or similar mechanical processes and infect other hosts.

That’s pretty much all that a virus does.

Notes

1) I said all our DNA is in the nucleus and controls everything. This is not quite true and I am sure some of you know that. We also have DNA in our mitochondria, the organelles in our cells providing us with energy at a biochemical level. Mitochondria look a little like bacterial cells living within our cells and some scientists think this is where they originally came from. It is suggested that a very early Eukaryotic cell absorbed and made a symbiotic relationship with a bacterial cell that was very good at making ATP (the unit of energy in most biology). This was so successful that the organism that did that out-competed all other Eukaryotic life and took over. And, over time the absorbed bacteria became simplified and specialised as the mitochondria. As a result, mitochondria have their own DNA. As do chloroplasts in plants.

2) There is really only one hard, absolute rule in biology. There is an exception to every absolute rule. See 1! Forgive me if I don’t cover all the exceptions in the rest of this post, but what I sat here is true 99.9837% of the time. And treat all percentages in documents with scepticism, many are made up.

3) The distinction between amino acids and peptides has always annoyed me. If “Amino acid” is the term for the building blocks of proteins should not a chain of amino acids be a “polyamino” or something? No, we have peptides/polypeptides.  A peptide has to be 2 or more amino acids as it is named after the bond between the two amino acids. A Peptide bond. Strictly speaking a peptide of between 2 and 20 amino acids is called an oligopeptide, and above that is a polypeptide. It’s just messy.

4) The ribosome may not drop off the mRNA. If the poly-A tail and the mRNA cap are intact, they my bind together to form a loop that allows most of the ribosomes to simply circle around the whole mRNA and make more polypeptide more efficiently. This might help curtail the activity of the mRNA more quickly as, when the poly-A tail or the cap are degraded (as there is some mechanism to degrade the cap too), then the loop is broken and Ribosomes can no longer cycle around. I don’t know the details.

5) The codon to amino acid mapping is very nearly universal. Almost all organism use the same mapping and it is one of the proofs that all life on this planet is related. However, there are some exceptions (as there always are in biology). If you want to nerd out on it look at this Wikipedia page on alternative codon translation tables.

6) The basics of the central dogma of molecular biology has been known for over 50 years. Here’s the start of the chapter on it from my 33 year old  “Genes 3” by Benjamin Lewin. Looking back at this book, which I pretty much knew cover to cover back then, I realise how much knowledge has leaked out my head.

This is the central dogma in my genetics undergraduate text book from 1988

Covid-19: The New Variant and the NHS December 29, 2020

Posted by mwidlake in COVID-19, ethics, rant, science.
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<<- Long term hopeful, short term worried

As I said in my blog post a couple of days ago, I’m very concerned about the new variant of SARS-CoV-2 that has been spreading through the UK and is now being found in countries all over the world. My main concern is that this could be what pushes our health services beyond the limit of what they can stretch to and, as a result deaths will jump up – and not just from Covid-19.

New Variant Impact

In my last post I highlighted the new variant of SARS-CoV-2 that is more infections (spreads more easily), but said that there was little evidence that it was any more fatal. Understanding what was going on was hampered at that point as we had hit the festive period and, with the best will in the world, everyone needs a break at some point. New data on hospital admissions, virus sequencing, case numbers were all missing or affected. Scientists studying aspects of Covid-19 were reminding themselves what their partners, kids, and pets looked like after what must have been a heavy year. Now the new information is coming out, as is the analysis by relevant experts.

There is a paper detailing this new variant by Public Health England which was published on 28/12/20. Much of the below is derived from that, but is backed up from many tweets and bits of evidence from the scientific community.

This new variant is know by a few names:

  • VOC 202012/01 – Variant of Concern identified in 2020 month 12, number 1
  • B.1.1.7 – the phylogenetic name of the variant (I think!)
  • 20B/501Y.V1 or simply 501Y.V1 – the identifier given by Nextstrain

B.1.1.7 has many mutations from the original SAR-CoV-2 virus (this STAT article states 17 mutations, the tracking page I mention below lists 17 SNP mutations, this overview by the CDC on VOC 201212/01 lists 20 SNPs and 3 deletions and seems to be the best source of information on this. I’ll explain all the mutations better in a later post) . Mutation is not unusual, viruses change all the time. Each time a virus is copied (and that is how viruses like coronaviruses reproduce, there is no sex, they are identical clones of their only parent) the RNA is copied and occasional mistakes are made and thus changes, mutations, happen. The most common change is a Single Nucleotide Polymorphism, or SNP. One letter of the 30,000 in the viral genome changes.

A single SNP change to the SARS-CoV-2 RNA does not seem to be enough to change the virus into a significantly more infective version (or more lethal, or more likely to infect children, or change it’s behaviour in a way to make it more dangerous). If it did, we would have seen this already – the virus has been so successful in spreading in humans and thus reproducing and so those SNPS occurring, that most individual SNP mutations that are possible will have happened by now (there is evidence for minor change by them though, but that’s for another time). It is going to be a combination of two or more changes I think that has altered the transmissibility.

B.1.1.7 has several changes to the gene that creates the spike protein.

The paper from Public Health England I reference reviews the data that was initially presented to the UK government (on around the 19th December I presume) and resulted in their initial analysis of the 21st, which this paper links to.  This review considers the degree to which the new strain transmits more easily and possible reasons why. It can  be summed up as saying:

  • This new variant is indeed spreading faster.
  • it is becoming the most dominant strain in all the areas it is in.
  • It’s ability to spread to others (secondary attack rate) is increased by about 55%.
  • It is not spreading faster as it is more successful in re-infecting people who have already had Covid-19.
  • There is no evidence it results in more hospital stays or is more fatal.

I’m not sure the evidence is yet firm that this new variant does not also increase the severity of the illness a little as there are too few cases to go on, but it does not like there can be a huge increase. Usual caveat, I’m no epidemiologist.

I’ve also looked at a paper by Nick Davies’ team at the London School of Hygiene and Tropical Medicine.

They considered 4 possible methods by which the new variant (they use the VOC202012/01 name) could be causing the rapid spread of the new variant

  • A) Increased Transmissibility
  • B) avoids current immunity
  • C) Children being more susceptible
  • D) shorter viral generation time

As you can see from the graphs, the model based on (A) Increased Transmissibility fitted the date better than anything else.

You may be aware of the new variant in South Africa that is also more transmissible. This is not the same as B.1.1.7, for example, it does not have the 69/70 deletion mentioned in Public Health England paper that is used as a proxy to identify B.1.1.7 in the UK population (again, more information later on the details of the new mutation). So this deletion either is not key to the increased transmission or else there are two methods by which the transmissibility can be increased (now, that’s a worrying thought).

There has been a lot of other analysis and commentary from the scientific community to back up the hypothesis that B.1.1.7 spreads 50%-55% faster.

Why Is 50% Faster Spread So Significant?

Why is this significant? Wouldn’t 50% more lethal be more of a worry?

No. The reason an epidemic is so scary and has such an impact is down to exponential growth. To use an extreme example such as exists before a new disease is recognised and steps taken to control it, If 1 person infects 2 people who infect 4, 8,16,32… Ten duplications later and you are at 1,024 infected people. If each person infects 3 then it goes 1 person, 3, 9,27, 81…ten tripling’s is 59,049. If you know how many people each infected person will infect (the R number) and how long it takes for an exposed person to themselves become infectious, then you can calculate how quickly the disease will spread and grow. So the transmissibility is key.

Adam Kucharski put it better than I can (if you are on twitter and you are interested in Covid-19 science, if you are not already following Adam then I highly recommend you do, and then follow some of the people he follows). This is how he explained it:

Here in the UK the number of cases and, more importantly, hospital admissions have been shooting up. You cannot compare case from the spring to now as testing now is orders of magnitude improved compared to the shambles back in April. But hospital beds occupied is a very powerful metric and can be compared. Up to a point.

I showed a graph in my last post about how many people are ill in hospital with Covid-19, going up to 24th December. The below is the graph up until the 28th December. We still don’t have data for Wales, Northern Ireland, and Scotland beyond the 22nd December – but England on it’s own ( 20,426) is not far off matching the UK peak of 21,683 back on 12th April. If we optimistically only add on 1,727 for Wales, 1,045 for Scotland, and 451 for Northern Ireland (their figures for the 22nd) we are at 23,649. I’m seeing a lot of stuff on social media and the BBC news about hospitals running out of capacity, cancelling routine work, calling staff in from holiday (and remember, this is staff who have nearly all been pulling extra and double shifts for 9 months already). We suspect are approaching 100% hospital capacity for the NHS.

Patients in hospital with Covid-19 across the UK, 28/12/20

Update, 30/12/20 – we now have the Welsh & Northern Irish data to 28/12, Scotland & England to the 29th . The UK total for the 28/12 is 23,771 (slightly above my optimistic lower threshold of 23,649, as is to be expected. Northern Ireland shows a modest increase that could just be random variation, all three other nations show an increase.

Patients in hospital with Covid-19 across the UK, 29/12/20

 

 

 

100% Hospital Capacity is a Really, Really Bad Thing

I said that hospital beds occupied is a powerful metric up to a point. Why up to a point? At some point that metric stops increasing so fast or even at all – but not because of a lack of patients to treat, but because you are running out of capacity in your hospitals.

I’m sorry, I’m going to go on a bit of a rant here. The below is why I get so vexed at people saying “I need to go on holiday” or “I must have my nails painted” or decide it’s OK if they have a party or that we don’t need a lockdown.

If you get Covid-19 and are badly affected, you may well need supplemental oxygen. You may also need treating for various blood clotting conditions, or to stop your immune system over-reacting, and several other things. That can only be done in hospital. If it is done, most people treated survive (though some of course still sadly die). If you are not treated, you will die. As some of you know, I had personal experience of this late last year when influenza type A and pneumonia landed me in intensive care for a week, on very powerful CPAP ventilators. If I had not had that treatment, I would not be typing this (or anything). So we can (and do) treat and save many people with compromised breathing and the other things that come with Covid-19. Until we run out of trained hospital staff. It’s not beds per se that are the issue, or ventilators, or really any equipment. It is people who have the skills to run that equipment, monitor you, keep you ticking over and otherwise not-dead whilst supporting the broken parts of your body until they heal. Once the capacity of the health service is exceeded, they have to pick who dies. And of course, we do not just have Covid-19, hospitals are dealing with all the other sick patients we always have – car accidents, cancer, influenza, septicaemia, heart attacks…

I’ve seen the stuff by some people about how “only” 377 or so healthy, young people have died of Covid-19. Part of me can’t be bothered explaining to them why they are selfish, clueless idiots right now but what I can say is if we run out of hospital staff capacity, you can be as young and fit and bloody callous as you like but you will die if you need oxygen treatment and do not get it.

I’ve seen some tweets by people who say things like “well, just get more nurses and doctors”. I checked, they are not made in a factory. Training to be a nurse is not like going on a week-long course to learn to use a chainsaw. Doctors and nurses and radiologists and lab staff (and all the others people forget about who are vital to the NHS) are trained for many years. Being an ICU doctor or nurse is particularly technical and needs months or years of training ON TOP of being a standard doctor or nurse.

The UK was desperately short of all NHS clinical staff before Covid-19. One of my closest friends organises the lab rotas for a very large hospital and she never has enough people to fill the rotas. She has to beg and hassle people to do more than their fair share of weekend and night shifts. They constantly have not just one or two but a dozen or more open positions for staff. I’m not getting political here but there was a crisis in care long before the pandemic.

If you see figures saying ICU capacity is at 90% you would probably naturally think “well, they still have 10% spare, it’s fine”. It’s not. One of my first jobs was writing bed management software for hospital systems and teaching hospital staff how to use the software. The software was a god-send for them. A hospital bed is not just a bed. It’s a type of bed, and there are several types in hospitals. Some are for children, most are for adults, some are powered to help move the patient about, some are specialist for ICU (such as being able to pass air around incapacitated patients to reduce bed sores)… And beds move. For my spell in ICU I was initially admitted to A&E and held in a storage room as there was no spare capacity. They brought a suitable bed to me and squeezed it into the storage room. About 12 hours later, 6 or 7 nurses took the bed with me and a shit load of equipment through the hospital to the ward.

You have to know who is in which bed, the consultant & specialty treating them. For very, very good reasons, the specialist or someone in their group needs to approve a lot of what is done to you in a hospital. To administer a drug to a patient you have to find the bed they are in and you have no time to go wandering around the ward as you have 101 other things to do. The same is true of feeding the patient. You have to track when a patient moves (either with their bed or moving from one bed to another) and you need to know where you can move them to, so you need to know what beds are spare or, more likely, probably going to come spare. I worked on another part of the hospital system, “notify patient as dead”. It was horribly complex, lots of stuff has to happen when a patient dies, for example some lab tests get cancelled, others get created. The bed is noted as empty pending a deep clean. Sometimes, heartless though it sounds, the staff need to know when a bed is likely to become available via that route.

The people in charge of beds need to know ASAP when a bed is free so they can try and do all the juggling above that I mentioned. The fewer spare beds they have the harder it gets to make use of the few spare ones you still have and move people around efficiently. Or even inefficiently.

When I moved out of ICU it was a rush job. Someone needed one of the very most critical ICU beds (yes, there are tiers to what we non-medics think of as ICU), they felt able to move another person into my intermediate dependency bed as they were improving – IF they could get me out of it and into the Respiratory Medicine ward. Which they did, at about midnight. The sticking point was I needed to be isolated to I could not give someone with COPD influenza and finish them off. Another complication. It being night there were fewer staff so only 2 people could be spared to move me. Admittedly, less equipment came with me but half of it (including a heavy oxygen cylinder) was on the bed with me, I had hold of something on wheels, the 2 nurses somehow corralled the bed and other equipment.

The point I am making is that the closer a hospital gets to 100% capacity, the harder all that juggling becomes, and you actually end up having to move patients to other hospitals – and moving a sick patient to a different hospital is generally not in the best interest of the moved patient – or discharge patients who could really benefit from being there longer (but don’t need it as much as the person who is dying that they can’t find a bed for).

I’ve only ranted about beds. I have no idea how they keep track of other equipment, plan who is allocated to do what, how to cover for say a member of staff going ill, a major road traffic accident when all ICU is full…

If we do not see some sort of miraculous downturn in hospital admissions (and all indicators are against this happening) I’m expecting the UK to be in full national lockdown in a week, kids returning to schools cancelled. If we hit 100% hospital capacity and are not in a strict lockdown, then our government will have failed us in this crisis once more.

Even more distressingly, we may see avoidable deaths.

 

 

Communicating on Covid-19 Again December 27, 2020

Posted by mwidlake in COVID-19.
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New Variant & impact on NHS->>

<<- Start of Original Post beginning in March 

After quite a break, I’ve decided to return to converting my notes & thoughts on Covid-19 and SARS-CoV-2 into blog posts again, but I’m going to do so in a slightly different format. Why am I returning to blogging on the topic? Well, people do still keep asking me what is going on and I’ve mostly been answering on Twitter or Facebook (or in person on the rare occasions I meet people!), but I don’t feel Twitter and Facebook are particularly good forums for explaining things. And writing it down in a way I feel someone with a little bit of scientific understanding can understand helps me understand and, more importantly, makes me check the scientific output to try and make sure I am right.

As for the different format, I’m going to do shorter, less comprehensive posts. This is because when I did this last spring/early summer I would spend a week doing a post that I thought would take a day and, by the end of the week, some things were changing and the post was just too loooooong.  If you feel something is missing from my future posts or you have any question a post prompts, please ask. If I can I will try and answer, or at least point you in the direction of a scientist or similar expert saying something about it.

On the subject of expertise, as anyone who has followed my blog knows I am a computer person (I specialise in the performance of Oracle databases). As ever I am going to stress that I am not an epidemiologist, not a virologist, and I have no medical qualifications. I have never been a working scientist (closest I got was I did a summer as a volunteer in a genetics lab before my final year at university, I mutated moss). What I do do is look at the output of scientists who communicate on Covid-19. I only listen to scientific and medical output. I do look at what the UK government says but I don’t see their briefings as a reliable source. This is not due to conspiracy theory, it’s more that (a) the UK government does not have a good back history of actually ‘Following The Science’ as they keep claiming (b) their job is not to explain stuff, it’s to get the population to do what they want them to do and yet remain as popular as they can (c) when a minister or one of the experts on the public briefings do explain something, they have to keep it simple and short.   

Given I am not an expert, why do I think I can explain to you what is going on? Well, I have an ancient degree in genetics & zoology and I’ve maintained an interest in science all my adult life. I’ve worked (developing computer systems) in or alongside the UK NHS for 7 years, in biological academia (mostly ‘the human genome project’) for 7 years, so I have a lot of experience in communicating with medics and scientists. For the last 15 years I have presented at conferences (and I get good speaker scores), written articles, done the odd webinar, and produced this blog. So I have experience of communicating what I do know to an audience.

If you want a refresher on Covid-19 (what it is, what it does to you) there are endless resources out there, but This summary I wrote back in March is still mostly relevant and it is interesting to see the predictions I made and which were right and wrong. Spoiler, I’m pretty good at saying how things will go for a few weeks (as are millions of others), I’m not so good beyond that, so I’m leaving that to the epidemiologists!

I’m hoping to put out my first real posts on the current situation on Covid-19 in the UK over the next couple of days, but I wanted to mention what is really concerning me and what helped prompt me to dig back into the scientific details again.

Long term – I’m really hopeful.

One thing I was wrong about was how long it would take to create a vaccine that was safe and gave good protection. I’ve never been happier to be wrong!

It’s a testament to the long hours and days of work of thousands of scientists, the worldwide sharing of information between scientific groups, the funding made available to them by governments & charitable bodies, and the efforts of the regulators & pharmacovigilance experts working to ensure Due Diligence in compressed timescales – i.e. that the vaccines are proven safe.

We have three vaccines in the West that are approved or close to being approved over a growing number of countries – 

  • BioNTech/Pfizer and Moderna/NIAID that use the new mRNA-based methodology. They need to be kept very cold (minus 70C and minus 20C respectively) but are approximately 95% effective,
  • The Oxford University/AstraZeneca vaccine which is a more traditional vaccine that uses a modified, harmless adenovirus and is less effective (work still being done on how effective: 60-90%?) but does not need to be frozen and so is much, much easier to transport.

Many more vaccines are still in development. Having a set of vaccines will be a real boon as, for example, the Oxford/AZ one will be a lot easier to administer in warm countries lacking in ultracold-chain facilities, but where such infrastructure is present, we can use the more effective vaccines.

Gary Myers corrected  my information on how cold the two mRNA vaccines need to be kept and pointed me to this article by NPR

Nine months ago I would have been overjoyed for a single vaccine that was 75% effective by the summer of 2021, so to have three by the end of the year and more on the way is fantastic.

But it is a massive logistical effort to roll these vaccines out and the impact on the spread of Covid-19 and our lives will evolve over the next 12 months. For the whole globe we are looking at 2 years probably and I am sure there will be bumps along the way, such as one of the vaccines proving to be not very long lasting so re-vaccination is needed for some.

One thing I want to point out is that there have been over 1/2 a million 5 million people inoculated (wow, that’s shot up so quickly) to date with very, very few contraindications (things going wrong) reported. I am not aware of any life-threatening reactions to the vaccines to date but they protect the vast majority of people from a life-threatening disease.

You can track world numbers for vaccinations at this “ourworldindata” site. I have not looked at it much myself yet but it certainly seems to give you the key information.  

Short term – I am very worried

I was already concerned that world figures for cases & deaths continue to rise, the figures in the UK are constantly going up, and yet more and more people seem to be wanting to believe there is no problem. And now we have new variants of Covid-19 that spread more easily, both in the  UK and across the globe.

In summary, as some of you will be aware, we have a new, more contagious, variant of SARS-CoV-2 in the UK, which is most prevalent in the South of England. It appears to spread a lot more efficiently than other versions and it has worried the scientific community. For once, the UK government actually responded very quickly to this change and they “cancelled Christmas”, put the South East and London effectively into lockdown and soon after announced many other areas would go into the new Tier 4 the day after Christmas. (To be clear, many scientists had already called for the proposed relaxation of social distancing for 5 days over Christmas to be abandoned and replaced with tighter controls, based only on the growing case figures – which Boris Johnson and his cabinet seemed set to ignore).

With the new information about the new, more virulent variant of SARS-CoV-2, many countries have stopped flights to/from the UK or brought in stricter checks and/or rules on isolating people arriving from the UK. France closed their border with the UK preventing (amongst other things) any lorry freight (as people drive the lorries). This island became pretty much isolated (and people started worrying about getting fresh salad, which tells you a lot about some people’s priorities).

Cases of C-19 in UK Regions since August

It seems some people think these national and international restrictions were brought in simply because the number of cases of Covid-19 in the UK were escalating quickly, but it was this new variant that has mostly worried other countries.

The graph is from an excellent twitter thread by Christina Pagel, based on official UK government figures. It shows how the last UK lockdown had the intended effect of suppressing Covid-19 in most areas, reducing the number of people affected by the disease (unlike the regional tier approach which had struggled to really reduce transmission). However, look at the black East of England, orange London and green South East lines. The lockdown had less effect there and by the end of lockdown cases were rising in these areas. Why? It could have been more testing being done (so you see more cases) or people ignoring the rules, or something else. It turns out it was something else, this new variant. Correlation is not causation, but the percentage of people with the new variant of SARS-CoV-2 is much, much higher in these areas. Lap tests have shown the new variant latches onto ACE2 proteins, it’s door into our cells, more efficiently.

At the moment there is no evidence that this new variant is any more deadly or makes people sicker, or that it means the vaccines that are currently being rolled out will not work against it, but time and more study will tell.

C-19 patients in English hospital 14/12. It will increase.

So why is this new variant a worry? Because if this new variant is spreading more easily (and the figure quoted by the media is “70% faster” but I’ll dig into that in a later post) it means the number of people who are ill will double much more quickly – and we are in real danger of flooding the NHS with ill people. All along, since this new disease reared its head, the overwhelming of healthcare systems has been the main worry, much more than the actual raw number of people it will kill and harm. That is what all that talk about flattening the curve was about in March & April, spread the people getting sick over a longer period so at no point do you run out of hospital capacity. The more infectious version of Covid-19 is pushing up the curve, and threatens to do so very significantly.

The graph to the left is for hospital beds occupied by Covid-19 patients as of Christmas Eve – the latest day we have figures for as I type. They are only just below the April high. In Wales, for which we only have figures up to the 22nd December, bed occupancy greatly exceeds the spring high. I am sure that if we have not already exceeded the previous national high for hospital bed occupancy UK-wide then we will in a very few days and it will get worse, as people catching the disease over the last week or two get admitted. Cases precede hospital admissions precede number of deaths.

The new variant is most common in the South East, East and London areas of the UK, but it is present across the whole of the UK. (In Wales there appears to be slightly different more-contagious version of SARS-CoV-2 but again for a later post.)

Here in the UK we are in for a rough ride and the government is going to have to bring in more restrictions to try and keep this new variant under control. 

New Variant across the world

What about across the world? Well this new variant is already present in many countries. It might have originated in the UK, it might not, this is still being investigated. The reason we do not know for sure is that the UK sequences a lot more SARS-CoV-2 samples than other countries, so they might not have spotted what we did. Again, I plan to expand on this in a later post.

The new varient, B.1.1.7, has been seen now in France, Netherlands, Singapore, Italy, Israel, Denmark, Australia. The list will grow daily.

I’m afraid the genie is out the bottle and, much as we saw with the original spread of Covid-19, with international travel and it having got out before we could close borders on it, it is probably inevitable that this new variant will take over in all countries where SAR-CoV-2 is spreading.

In South Africa there is yet another more virulent strain, with some of the same mutations the new UK strain has, which seems to have arisen independently. I have no idea why more than one highly virulent strain has occurred in relatively close temporal proximity (same time) in different locations, it is probably just bad luck. Genetic mutation is random and directionless (well, with a few odd exceptions that as far as I know do not apply here). This other new strain is known as B.1.351

Both variants can be tracked at this site, which is where the image to the left is from. Updates are a little slow at the moment due to the time of year but, even with it being Chistmas, the people behind the site have added more information. Scientists, nothing stops them for long.

I think we are at a crucial point:

  • Vaccines are on their way and that is brilliant.
  • World wide we were already struggling to keep the Covid-19 situation from getting worse.
  • The new variant(s) are increasing the spread rate, possibly significantly.

Despite my reputation for it this year, I don’t like being all doom & gloom, but I feel right now like I did at the end of February/start of March. Very anxious about how this is going to play out for so many people, especially those who (for whatever reason) have decided Covid-19 is being blown out of all proportion or is not going to impact them.

I cancelled Christmas before the government did, it was not wise to go see my mother and brother, even though we all keep ourselves fairly isolated and take all the proper precautions. I think no matter what, for the next 6 months until the vaccines are making more of a difference (and by this I mean reducing the stress on the NHS by protecting those most likely to get critically ill, as opposed to herd immunity), I’m going to be a hermit, read books, sort out the garden, and keep watching what the scientists say.

I think Christina Pagel summed it up perfectly: