Hello, and thank you for listening to the MicroBinFeed podcast. Here, we will be
discussing topics in microbial bioinformatics. We hope that we can give you some
insights, tips, and tricks along the way. There is so much information we all
know from working in the field, but nobody writes it down. There is no manual,
and it's assumed you'll pick it up. We hope to fill in a few of these gaps. My
co-hosts are Dr. Nabil Ali Khan and Dr. Andrew Page. I am Dr. Lee Katz. Both
Andrew and Nabil work in the Quadram Institute in Norwich, UK, where they work
on microbes in food and the impact on human health. I work at Centers for
Disease Control and Prevention and am an adjunct member at the University of
Georgia in the U.S. Right, so this is the very first episode where all three
MicroBinFeeds are together, and this is the first time it's ever happened. Every
other time has been on Zoom, so thank you very much to Nabil and for Lee, you
know, for flying over from America just for this episode, but we're also joined
by Torsen Seaman as well, who is going to keep us on track. So today we're going
to talk about loss in translation, the barrier between research, mathematics,
and what actually happens in the real world in public health. So Torsen, do you
have any questions for us? We haven't seen you in a long time, mate. You were
back on episode six, you know, it's been a few years. I know, like most of you,
I've been hibernating for various reasons, COVID, pandemic-related work. I'd
love to sort of hear what kind of trials and tribulations and fun you had
working in COVID, so we can compare war stories from the pandemic. Not the
boring stuff, the fun stuff. The fun stuff. Well, I mean, we had a lot more
COVID than you guys, you, you know, being a huge island, you know, kept it all
out, whereas we had a constant flow and a lot more business. Britain is also an
island. Don't tell anyone that. It's true. We did close our borders, but we had
lots of citizens returning, return travellers. So return travellers were all our
introductions. So that was something quite different to what many countries
experienced. So you had high quality epi then, you know, to trace all of these
back into quarantine and you kept it all out no matter what. Yeah. We had lots
of good epi about hotel quarantine and travel history, and yeah, even things
like picking up in-flight transmissions was quite interesting. Serious. So that
was in the early stages of that. That was of great interest to the federal
government, like, were there being in-flight transitions? And we had a couple of
analyses where, yeah, there was a lot of evidence that the transmission actually
happened during the flight because, you know, two separate countries, people
getting on the same plane at Singapore, for example, which is a big hub for Asia
Pacific. And then, you know, looking at the data, genomically proved that it
couldn't have probably happened any other way except within the aeroplane
itself. So that became a big concern. And I think that resulted in, you know,
some policy around masks and separation of people in aeroplanes and high
filtration levels and things like that. And also the flights are long enough
that you could get on a plane and 17 hours later, you know, you won't go from
negative to positive and, you know, highly symptomatic. Yeah, I wonder if they
were doing, rat tests weren't really around yet at that point, but it would have
been fascinating to do rat tests every six hours during the flight to see the
progression of the disease. If you were a PCR and a rapid PCR on the plane,
could you even do that? I'm not a lab person, but I'm sure you could put a lab
in a small lab in a box. We gotta try that. Do you need a centrifuge? I think...
To spin down? Let's not reveal how ignorant we are at this point. Must have
biology or something. Well, I recall, you know, the back in the day when MinION
was being used in the field by ecologists and stuff, that, you know, one of the
arguments was, well, the MinION part's easy. How do you extract the DNA and make
the sample? And, you know, there was this... Nanopore had their Voltrex that
never really quite worked. But I heard that some people in the field, you needed
a centrifuge and they were using their four-wheel-drive axle, they were using
the wheel to drive a centrifuge from the four-wheel-drive. That's brilliant. So,
yeah, that was pretty cool. So I think a centrifuge must be an important part of
the spinning down process. I remember for Nanopore, some people going out to
like schools to do demos and all that and they'd just heat stuff up in their
hands, you know, just hold and the body heat would, you know, warm it up to the
required temperature. Ah, so instead of the old-school way of thermo-cycling
from moving from water bath to water bath, they would, like, use their hands?
Yeah. Oh, that might happen. You've got solid spinners actually now, like, with
your little manual centrifuges. Could work quite well. Quite cheap. I think you
do need the centrifuge, though, for certain things. Like when I was, 25 years
ago, when I was in the lab, we'd have to purify DNA using that kind of technique
with the kayak heads and stuff. So we'll have to try it. Can I actually... Lab
in a box on a flight. Lee here has pointed out that he has done some bench work
in the past. Have I, Nabil or Andrew, have you done any lab work? Ever? I
stopped doing biology when I was about 16, so I did zero bench work. I've done
two PCRs and one of them worked. So, yeah, I have actually done... I have done
seven days of molecular biology training. Our Monash University had a famous
annual course called the Recombinant DNA Training Course, and it was... A lot of
people used it for their continuing education to get refreshed. And I asked if I
could do it, because I wanted... I was only in bioinformatics, and I wanted to
get a feel for what actually happens on the bench so I could better understand
the processes. And so they let me do it. And, you know, you got paired up with a
tutor. Yeah, we did everything. We did DNA extraction, virus extraction from a
plant. They had this infected plant that they gave everyone a leaf and you had
to extract DNA and virus. Had to clone a gene into a vector. Had to express
that. Did capillary sequencing. My sequence turned out terrible. It didn't work
at all. It must have been a mixture or something. But, yeah, I really got to do
it all. And I actually won the destruction award because I dropped my timer and
it smashed and the battery fell over the lab floor. I overwhelmed my pipette on
one of the settings and nearly broke it. And then I spilled... When I was
flaming... You know how you do this flaming thing with the bottle to keep things
sterile or whatever? I spilled alcohol on the bench and the bench caught fire.
Oh my gosh. This is the destruction award? Destruction. Destruction.
Destruction. Yeah, most students do one of those things. Yeah, I did all three.
And so it made it clear that bioinformatics was the right career choice for me.
No one can say you're not comprehensive and thorough. Did you say you did this
all in a week off? Yeah, in a week. So it started on Sunday. It started on
Sunday and it went from 8pm to 6pm every day. You're doing multiple experiments
in parallel and theory and practice. It was the most intense week of my life.
And the following week I fell ill with cytomegalovirus and I was sick for three
months. I think the stress of this course must have triggered something. And I
was out for months. With fevers every night for three months. That's how much...
That's just from lab work. Lab work induces fevers. Maybe it was an infected
plant. No, no, I think it was something... I was told that CMV, cytomegalovirus,
I mentioned it to a couple of colleagues and they said Oh, you're a new dad,
that's normal. And it turns out that new fathers... Most of the population has
CMV already, latent. But about 20% of the population apparently doesn't have it.
And clearly I didn't get to kiss enough girls or something when I was young. So
I never caught it. So he said it's common in new fathers because babies get it
and they're not affected by it. And they shed it in their urine. And I was
changing a lot of nappies. And he says it's classic presentation. New dad, CMV.
So no other doctor said it. As soon as I said it, he said, yeah, new dad, I see
it all the time. So yeah, I wasn't a new dad at the time. Lack of sleep, intense
course. If you don't have kids, then obviously, just to paint a picture, when
you're boys, they piss everywhere when you are trying to change your nappies.
Yeah, a lot of airborne streams of fluid. Absolutely, yeah. Can confirm, it's a
different kind of aerosol. I promised I washed my hands, but he obviously can't
account for everything. I had an experience also when I first joined CDC. I was
one of the first bioinformaticians. And I was going to be at the computer all
the time. And then they said, no, you need to learn how to run PFGE. And they
forced me into the lab for a couple of days. And I did run PFGE. I did quite
well. I can find that gel somewhere, probably. I had really good bands. They
complimented me. And I never wanted to go back again. But it helped me be a
better member of the team and to be in there with everybody else. Yeah, I had a
great appreciation for what goes on. Especially where errors can creep in and
why things don't always work out. I think it's a great exercise to go through.
Whereas my experience in the lab is I have posed for some photos with a pet and
some buffer, you know. I've done it a few times now to make it look like I'm a
scientist. We're not allowed to take photos of anything in the laboratory. It's
against the law. You need to get special permission to take photos of any lab
stuff It's a public health lab. Biosecurity related. That's like legislated or
is it part of the policy? It's probably just the health law. I don't know
actually. So during the pandemic I found it was quite interesting going from
research and then seeing insights into public health labs, you know. Because in
research we just do things kind of not willy-nilly, but you know we're more
adventurous with what kind of protocols we'll do. And we'll tweak stuff left,
right and center. We may not run controls every time. Whereas in public health,
you know, it's quite a different environment as you guys well know. Having moved
from research to public health, I also noticed that as well. It's very
interesting.  frustrating when you first start. You feel like nothing, you can't
get anything done and it's too much, too many rules and steps but it's all for
good reasons. I mean these decisions, the decisions that get made from what we
present are real decisions. So in the pandemic like our genomic results directly
discovered a major hotel quarantine outbreak and also there was a big giant
residential tower that was immediately locked down and due to the results that
we presented and you know this affected people being locked in their building
for like weeks and so yeah you want to make sure 100% that what you're
presenting is correct. And not just contamination or a sample swap. Exactly.
It's a little flattering that they listen to you though also. Yeah we'd already
built a good relationship with our department of health you know doing genomics
to foodborne pathogens and they built a lot of trust in the results and it
wasn't just a genomics we always did in consultations with the epi's and you
know the department admin and so that relationship really was established before
COVID came along and then with COVID they really put a lot of trust into us and
we took it seriously. We didn't just like you said present results willy-nilly,
we sort of poured over them, made sure we were had some degree of confidence in
what we were telling them. From the bioinformatics point of view it wasn't
really, a lot of it wasn't my responsibility. The epi's took the, the genomic
epi's took the front of the questions and stuff but yeah we were there in all
meetings, there were bioinformaticians in all important meetings in the pandemic
and now in all department meetings there's always a bioinformatician because we
need that you know that support to the epi's when that questions get asked and
they you know they're trying to assess how real the results are then we can sort
of say you know with COVID there's missing data, so samples can migrate in the
tree and things like that. So it's just been an amazing transformation from
bioinformaticians being in the basement type approach to now they're being in
the front of house as a first-class citizen along with the epi's and the medical
microbiologists. Incredible. There was one study that you did that I came across
and actually this is the first chance I have to to tell you about it. I think
when I was pulled into the response for COVID one of the things I had to do was
figure out if people could get reinfected and you know that's that's like a
lifetime ago now but back then we had I think about like three months of data or
something this is all published and I had to help them with the genomics of
figuring out if if somebody like if we had we had certain cases we could look at
before and after like infection one infection two and we could look at the
results in between also and figuring out if it's the same genome in infection
one infection two and I was like maybe I'll do like an all versus all comparison
see what it looks like I'll check the literature and see if anyone else has done
this and I found one of your papers and you did exactly what I was thinking and
you already published it in a pre-print do you remember this one was that a
hospital a small number of samples um memory has been a bit damaged from COVID
pandemic like I'm really struggling to remember all the projects we did I don't
remember so yeah I don't have this in front of me either I think you had like
but there was one where we had multiple samples of patients over time and
looking at intra host diversity versus inter patient diversity and stuff like
that it was really hard it was a hard project because you know the data is a bit
questionable and I think we only really looked at it from the consensus level
what we should have done if we had times to go back and look at the raw fast q
data because two separate infections one of them if it was close enough could
have been a mixture or a minor allele fraction in that original sample that then
became the dominant clone in the second infection like was it late in all that
time or was it a new infection that yeah that's a common question we got and we
just didn't have time to look at most of it but I think there's a lot of people
now look going back to data that's been deposited like as I know the US and the
UK have been awesome at depositing their fast q data so a lot of these studies
can be done assuming the metadata about what cases are from the same patient is
available yeah we had very little metadata especially because we had to get from
the states and get permission and all that but yeah you have to make sure the
metadata is good because you can't just you can't go at it alone with just
genomics and you get at the siren project which was to sample healthcare workers
and then sequence them so the idea is that healthcare workers would first in the
front line you know if they're if there's an infection stable ones who were
infected first and I did it fine some at the end of course I've had to cover
three times now so I can tell you you can get reinfected but there's all these
thresholds that put in like you know you have to have 90 days between the first
positive test and the second just to make sure try and make sure that you know
you're not just seeing the same thing again that's just popped up again yeah
well actually talking about we haven't caught up in a few years so yeah so so
coming out of hibernation you know from the last three years of finally getting
to meet you guys in person again I speaking to Andrew, Andrew you were telling
me that you were involved in the COVID response and you're at a research
organization I just assumed that only public health labs were involved in the
COVID response and can you tell me a bit more about like how you were involved
in the UK crowdsourcing effort yeah so basically a conference you go to every
two years ABPHM and essentially half that conference just were pulled into the
Cog UK project and because you already have a new most people are working on
bacteria actually and so it was just all these pre-existing links were tapped
very rapidly by you know like Nick Loman and Sharon Peacock and people like that
all the big names and they're all folded in and so we just became one of the
labs doing sequencing for the Cog UK project and yeah like I shared an office
with a guy called Tom Connor who part-time and he was doing public health Wales
and so he was like oh you know do you guys want to come in on this I said yeah
sure why not we can do sequencing you got sequencers you got staff everyone
wanted to help you know everyone was super enthusiastic and so that's how we
initially got into doing the sequencing and the idea was basically everyone
would tap into their local hospitals and we shared campus with the regional
diagnostic unit for doing viral testing and so we could get samples very easily
and so that's how that kind of got started and then it kind of snowballed from
there you know we're doing more and more and we're doing mathematics analysis
and then we started doing national surveillance and we're doing international
cities so you know it all kind of expanded from there and we're a research you
know but we're doing you know production level stuff so every week in week out
we have to get samples in and out the door and do it right and you know all the
additional quality controls that you'd have in a public health lab we had to
start enforcing ourselves where did those protocols come from were they shared
with you or and how did the governance of the data work like it was made up on
the fly everything you know everything happened at pace you know so the
protocols came from like josh quick he developed the arctic protocol we just uh
basically parmers made up slightly in advance and because we figured we'd do a
little bit of this and got them made up and then they're just ready to go you
know and we're actually up and running very very fast within about eight days of
giving an odd we're up and running sequencing in production which is kind of
cool what slowed us down was paperwork but even that was done super fast you
know all the ethics all the contracts everything was signed like it was all
expedited very quickly and we're talking like march like early 2020 right we
started sample collection on the 8th of april 2020 and then we finished
sequencing mid-april 2022 so we did over two years two years every single week
including christmas yeah i still remember february the 14th 2020 valentine's day
in melbourne it was a friday and my boss said to me toss you and the bnp should
probably not come in next week we might have to work from home for a little
while two and a half years later we're still working from home still sequencing
carbon still reporting carbon yeah we got out of that thank god but it was a it
was a push it was a sprint right till the bitter end you know and we got more
and more samples coming in because you know they were still trying to sequence
all the omicron and whatever and then it just kind of luckily people said okay
we don't need to sequence everything we can you know scale back and you know
give everyone a break and researchers can go back to doing research rather than
public health i know a couple of things we we probably borrowed a couple of
things from you like i i think that our public health labs saw josh quick's um
protocols.io and they they adapted it for themselves and and maybe a few other
things and i thought it was kind of genius to go straight to something like
protocols.io to to make it kind of crowdsourced absolutely yeah it's very handy
yes agreed that became a great resource for lots of labs around australia new
zealand you know the midnight protocol the jse the protocol arctic protocol and
so on so you too okay we've opted around as well correct yeah we have corona had
we developed our own so in terms of uh data governance though we weren't given
sensitive patient information we were usually given a lab id from the clinical
lab so they knew so when we said this such and such was in this lineage and such
and such was in that lineage they knew what that meant but we didn't know much
more than say the patient sex and which county it was from or you know things
like that so it's quite vague for us how secure did you have to be with that
data because a lab and a lab name and a lab id if there's records at the lab the
pathology center they can link that to so you have to be very careful so the nhs
the national level it people came in and audited climb which is what we're using
the the virtual  machines we were using to make sure it was secure enough and
then you had to have a two-factor authentication brought in. But you're right, I
mean it was pseudo-anonymized but it wasn't fully anonymized. So we had an
elevated access and you had to sign a lot of contracts and whatever and you had
to promise not to try and reverse engineer the names. But the UK passed
legislation to get rid of all the privacy concerns. Because it was a public
health emergency, usually it was enough to be able to go back to the hospital or
to public health authorities and say this is the ID and then they would look it
up for us and say okay, you know, they would do the hard work of linking all the
people and the information and all that. Wow, that's very impressive that all
that stuff was expedited and permissions and it all just kind of worked. That
didn't happen to that extent in Australia. It was a lot of hard work. And some
people, like my colleague Justin McGrady who was another PI doing the wet lab
side initially, he was ringing random public health people and trying to go
through and find the exact people he could talk to on the ground who would give
him answers. And he did in the end and it made life a lot easier. We could go
direct to local people to discuss outbreaks and cases that we were seeing rather
than having to go to maybe a national structure and then back down again and
it's a few weeks later by chance they've passed the message along. And when you
had to report these results to hospitals or to public health units, was there a
language gap? At first, yeah, I think so. And we've got to remember COVID, what
you were reporting about COVID changed over time, right? So initially you were
talking lineages and everything were in separate lineages. You didn't have
variants. There were no such thing as variants of concern. Remember in the early
days, you had lineages and you had proper epi and you had differences between
them and you had distances between each of those lineages that you were trying
to communicate. And then it switched over to all this VOC stuff where it's just
like, you know, alpha, beta, whatever. And it was just like, which one is it? So
that changed over time. But initially there were a lot of gaps of, is this
related or not? Because you can say, you can just read off the number and say,
well, this is two snips away or three snips away or whatever. But then obviously
that's not a meaningful thing to a clinician They say, well, is it the same
thing? Is it, is it, does that mean this patient got this from this other person
or not? And I think Andrew did a lot of reporting back. In the early days, I
didn't know what to report. I was making up as we went along, to be quite frank.
And so in the early days, I was telling the local infection control doctors and
the local public health authority. We didn't, I didn't know what to report. So I
ended up doing things like, say, given the local medics in this county, we were
seeing 10 different clusters or a hundred different clusters and it's going up
and down, you know, kind of like a weather forecast or, you know, an overview of
what's kind of happening in the region and then which, which areas have hotspots
and which connected stuff and which don't and things like that. And then the
first real report that I remember had impact was on care homes where we were
asked to look at a particular care home which had a high mortality rate. And
they want to know, is there SNPs in there that are making it a problem? And when
we actually looked at it, we found there was like this particular lineage of two
SNPs that were unique. And then we looked on a map and we could see a heat map
of the postcodes, the zip codes, and could see that it was, you know, very old
people over the age of 80 in particular little places on the map. And I was
like, hang on a second, there's a problem here. And then when we went and looked
further, there were actually care homes, six different care homes, and the care
homes were infecting each other. And they're doing very well at keeping out all
the strains and clusters from the community, but not from infecting, cross-
infecting up the establishment or anything like that. So that was kind of our
first kind of impactful thing. But then what we found was it took weeks to get
the public health body interested in it. And by that time, obviously the
outbreaks had finished, but we then had the established link so that, you know,
next time something came up, we could actually take action immediately. So I
don't know if I can give the detail, but at the time, the real world reality
was, was that you had lockdown, so people couldn't see their nan in the care
homes. So there wasn't like a community transmission. But then the care home
staff were all on rotation amongst the different, you know, different sites.
Exactly the same problem in Australia. Agency workers that move between sites.
Yeah. And so when you, in hindsight, you go, well, obviously that's a problem,
but I guess the logistics and mechanics of it, like how else are you going to
staff the care homes though? Australia banned, we banned it in Victoria,
Australia banned working in multiple aged care homes, I believe at some point.
Wow. To restrict that inter-home transmission problem. Yeah, but that was, yeah,
that was, that was like. But there were bigger problems, like people weren't
being paid if they were sick, you know, or had to self-isolate. And like care
home workers are not paid a lot of money, it's usually like the minimum wage
type jobs. And so there were those issues that had to be addressed as well.
Yeah. Did UK introduce legislation to help those people? Yeah. Australia also
did similar. We had, you know, salary support for when you had to go on COVID
leave and stuff, you could just fill in a form, no questions asked and you would
get your two week salary. Yeah. Then it went the other way and they went for
intensive testing. And then people worked in care homes and in some cases
residents were being tested intensively and those are being directed to
particular testing sites and testing centres. And then they were being sequenced
as a priority. So, you know, they went from one extreme to the other. So bad
surveillance, really good surveillance. Can you tell us a bit about the states,
Lee? Like, given, I know you work for the CDC and the CDC isn't a central
authority, there's all state labs and county labs and how, what, what, what was
CDC's role in the sort of the pandemic that you, as you understand it? I am, I'm
going to say as much as I can say, and then like, I don't think I know enough.
Yeah, it's a hard question to represent a whole country of 300 million people or
whatever. It's so federated. It's so, we're, we, we supply a lot of information
and help coordinate a lot, but then the state health labs are really, they're
the actual authority for most things that happen, especially with COVID. And so
I don't know, I guess we, we, we provided a lot of support. At one point I went
back to the COVID response as the technical team lead, actually for the, for
helping out with bioinformatics in the states. We got a lot of stuff done as,
when I was technical lead, I was able to coordinate with a state lab and a few
partners who adapted Josh Quick's protocol, especially Joel Savinsky, and were
able to come up with other protocols and coordinate with other people to, to
basically make something more centralized and help out the states more. And, and
I don't know, just overall, we, we did help coordinate with bioinformatics, but
it's, it's coordination, you know, it's not something I can be like front lines,
like how you guys are describing it with, with the, being front lines with like
politicians or decision makers, not all the time. Yeah. I mean, Australia is
also a federation. We haven't, we only have seven or so states compared to your
50 or whatever. And yeah, we faced, we don't have a CDC, so we don't have a
national, like official kind of CDC. And there's actually talks right now that
to set up an Australian CDC for future pandemic preparedness, but they'll never
have full authority. And I think we would have the same problems you have. We
don't have full authority over the states, but you have a more coordinating role
and a role in sort of kind of getting people to agree. And I guess mostly for
shared data. Can you tell us how, how the counties shared data or the state left
shared data? Was there a central repository or how did, how did it work? Or was
it more ad hoc? I, again, I don't think I can speak totally towards it just
because of my lack of knowledge. There's a lot going on, but eventually the
states and local health labs got coordinated enough where they were, in the
beginning, they were sending samples to CDC to get them genome sequenced. And
eventually they started all doing it on their own and those sequences all got
deposited with either ingested or NCBI. And so we were able to coordinate on
that level. And what about you guys in the UK? As I understand it, kind of the
England, public health England, which has now been renamed, right? Yeah. UK HSA
health security agency, but in the UK as well, it's four countries with
different laws and different ways of doing things, you know, because public
health is devolved to nations. So like Wales said it very differently to
England, you know, but obviously different sized countries, Wales decided, oh,
we'll sequence everything. We'll do it through one system, you know, one kind of
coordinated effort. And that worked really, really well. Is that the COG UK that
we all heard about? Well, COG was sitting outside of that and talking to each of
the nations and maybe facilitating data sharing in a way that might not have
happened if they were just trying to do it directly the old fashioned way. Okay.
So COG UK was sort of a bit like CDC coordinating the sort of the members. We
had nowhere near that kind of, no, it's just a bunch of ragtag academics
sticking their nose where it doesn't belong. You were invited. It did belong.
And in Australia, we kind of rapidly built working groups and committees, you
know, with representatives from every state. And so, yeah, we kind of had to
build that infrastructure just like COG did, I guess, in a way. It's interesting
in other countries, because we've had people from, talk about their COVID
responses. So people from Canada and so on.  And it's interesting to note that
health predominantly is considered a provincial problem. I guess the philosophy
is that a particular region will have its own specific health issues and you
need to fund it accordingly with that and you need people there on the ground to
actually explain what's going on and they should have autonomy over it. And
what's odd is that that worked, but that doesn't work in a pandemic where the
pathogen doesn't care about your little provincial borders. It doesn't
understand your jurisdictions. And a lot of agencies had this issue that they
didn't have this open data sharing agreements. They didn't have MTAs, all the
sort of bureaucratic stuff to be able to talk with each other properly. And
often it was some other entity that was initially being a broker between all of
them. So in the UK, you had Cog that came out from outside of that doing it. You
had OzTracker that was coming outside of doing it and so on, like all these
different, it came out. And on the UK side, what happened over time, as much of
what Lee was saying, was a lot of it was on the Cog partners. And then slowly
the capacity was built within each of the health agencies and then we've given
it back to them over time. Can I say as an outsider to UK, I had no idea that
each of the countries, the laws and everything are at that level. So it's
interesting that it's kind of evolving to CDC. I still don't understand because
I'm talking as an Australian, I don't get it. It's like the United Kingdom is a
country, but then Scotland and Wales is a country. It's a country within a
country. It's like, okay. You were born in London. Surely you should know this.
Yeah, but I left before I went to school here, so I didn't get it explained to
me. Yeah, it's quite complicated. British Isles versus United Kingdom versus
Great Britain. Is it okay to say British Isles these days? I don't know. Well,
the Republic of Ireland isn't that, so no. No, so there you go. I don't know
what we call it. We forgive you. You're an American, so we expect you to be
ignorant of the rest of the world. Lee has finally learned how to pronounce
Norwich after a couple of years. Yeah, but we're not changing the intro. And
what's that city in the Midlands of England that starts with Berm? How do you
pronounce that? Zero clue. Okay, so that's zero clue because it sounds like
you're about to send me a trick question. Is it Birmingham? Yeah, that's pretty
good. It's not Birmingham. That's in the U.S., and Birmingham is in the U.K.
Okay, that was an on-the-fly guess because I thought that was a trick question.
I'm lucky because in Australia we have a lot of U.K. place names, so we've
learned how to pronounce everything. But even Australians don't know how to
pronounce it. I lived on Greenwich Crescent many years ago, but everyone would
say Greenwich Crescent, and it just came to me every time I heard it. And we
should probably delete this bit of the rant from the podcast. No, go for it.
Keep this. I just learned a few things during our snack break from the hackathon
where it's like Leicester instead of Leicester or something. Leicester,
Worcestershire. Worcestershire. Worcestershire sauce. So I'm learning a few more
of those things. And then how do you pronounce the city where we're in right
now? Bath. Bath? Not bath? Everyone has been saying bath to me on the way, and I
can't bring myself to say it. Should I be saying bath? There's a divide in the
U.K., so, you know, there's our consensus. But it's dance versus dance. It's the
same thing. It's a common vowel, different regional dialects. Even in Australia
we have a division on the vowels, some of these vowels. Dance, trance, and dance
or trance. Like, I'm a trance dance person, but if you go to Adelaide in
Australia, it's the other way around. How would you say it? I say bath. I say
bath just to annoy people. Because I think that's meant to be the lower-brow
pronunciation. Interesting. That's why I say bath. I just say bath. Bath, bath.
Stuff it. And do you necessarily pronounce it the same way as if you're getting
clean at home in a tub? Yeah, yeah. To me they're the same. I take a bath. Well,
you're going to see the Roman bath soon enough. You know, I've done some of
them. I keep having to tell people, you can't swim in the Roman baths at bath.
Well, there are special places I'm sure you can go where they give you the Roman
bath experience. But not in the actual, you know. Because there are some, you
can visit Roman baths, but you can't actually swim in them. They're 2,000-year-
old baths and you can still use it. Cool. Has it been cleaned ever? I should
hope so. Well, the water is a strange color, you know. That's an indication that
it's not very safe. Is that not spring water here? It's kind of bluey, which
usually means it's heavily alkaline. Like so dangerous that you can't go near
it. I've been noticing the tap water tastes like maybe a little sulfuric. Is
that? No, that's just a weird thing of the UK. They love bore water. Okay. Like
it rains so much here, but like for an Australian that's really bizarre. Also
the water here is very hard. It has a high salt content. Soap doesn't lather
here because of the water. But in Australia, our water is soft. We don't have a
high carbonate or water salt content. So soap lathers are probably crazy. Nice.
Good thing you don't have hair tossing, otherwise it'd be wrecked by the time
you leave. Yeah. I'm saving a fortune on shampoo. Speaking of pronunciation, how
do you say data or data or phage or phage? Rooster or rancher? Oh, man. I
change. I flip and change. Data, I used to say data only, but now I say data.
Like I got, you know, commander data on Star Trek, but it was data. And then
what was the other? Phage, phage and phage. I say phage, but sometimes I change
to phage. I sort of adapt to what people around me are saying to fit in. Yeah,
yeah, yeah. Phage data. It is rooter in Australia, but I just can't make myself
say it, so I just say router. Well, router might be considered the wrong thing
in Australia. Yeah, it's referring to an activity in Australia. Oh, didn't know
that. Well, rooting refers to when two people really love each other. Yeah, so
when that packet is being rooted through here. Yeah, it means it's royally
stuffed. Well, there's a famous Australian meme to do with whether you should
have a comma, the Oxford comma, which you may know is the comma before the last
and in a list, whether you have a comma or not. So what's the famous Australian
thing where it's a picture of a wombat and it says, eats roots and leaves. It's
got two meanings. We have eats shoots and leaves for a panda. Yeah, yeah, I
remember. Now, you might not believe us, but if you want to validate it, I think
for one of the football world cups, they had a promotion, which was they had a
big banner and they said, like, root for your team. And in Australia, they
changed it to, I think it's like cheer for your team instead. So all the
Australian publicity stuff literally changed the word just because they realized
that we can't say root for your team because that just, we don't want to
encourage that. Because it also has connotations about what football players
should do the night before a big match, whether they should or they shouldn't be
allowed to. I think this is a thing in baseball. They have to relax. Different
coaches have different rules, I believe. We horribly, horribly drifted off. We
were talking about serious, serious matters. You have pronunciation problems in
the US as well. Like Arkansas, not Arkansas. It's our Kansas. Arkansas. Yeah,
it's Arkansas. But then it's Kansas. If it's Kansas, why isn't it Arkansas? I
know. And the other thing is I found out that people from Missouri, a lot of
them don't pronounce it Missouri. They say Missouri, Missouri. They don't say
Missouri. Missouri sometimes. Missouri, yeah. Missouri, yeah. Interesting. Yeah,
yeah, yeah. But not from that part of the country. So everything's a little
foreign to me when they bring that up to me too. It's like the UK versus all the
individual countries confuse me too. That's where we were. What is the UK to
you? What do you think the UK is? The UK to me is the place I fly into. What is
the UK? Is it a single country? It's not a country. Is it the United Kingdom?
The UK to me feels like a country. But I guess it's obviously wrong. But it
feels like it's a country. What country are you in right now, Lee? Tell me. I
would say I was in the UK. But I know the answer is England. So it's the United
Kingdom and Great Britain and Northern Ireland. So you are in the United
Kingdom, Great Britain and Northern Ireland. In England, you're in Great Britain
as well, but which is a big island. Okay. And you're also in England. You're in
Europe as well, but not in the European Union. Yeah. So England, Wales and
Scotland are on the same chunk. But Northern Ireland is on a separate chunk.
Yeah. With Ireland. And I've... That's right, there's nothing else on that
island, right? No. The Isle of Ireland.  But then, what are the other islands
like? Channel Islands. Yeah, so there are Crown Dependencies and... There's
Jernsey, Jersey, Isle of Man, Isle of Wight, the... Does that have tax evasion
things there in any of those? It's not a tax evasion. They set their own tax
laws and they just decide not to, you know, charge people tax. Nice. Yeah. So
they are Crown Dependencies, so the Queen is head of state, but they're not part
of the United Kingdom. But they're part of... Great Britain? Yes. Yes. Well, I
don't know. There's a table that tells you what... There's a... There's a
matrix. There's some kind of complex Venn Diagram. Yeah, Venn Diagram. That's
the one. Do you think Charles has to learn all that before he becomes king? I'm
sure he knows it already. He's been... He's been an understudy for the last
seven decades. So thanks, Toss, for joining us today and thanks, Lee, for
actually seeing you in the flesh for a change. Yeah. Did we say this already
that this is the first time that we're doing this in person? Doing this in
person all together. Let's catch our mind, everyone. So yeah, and we were just
talking about just catching up and seeing what we've been doing for the last few
years and talking mainly COVID because that's what we were doing. So yeah. See
you next time. Great to talk with you again. Thank you so much for listening to
us at home. If you like this podcast, please subscribe and rate us on iTunes,
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podcast was recorded by the Microbial Bioinformatics Group. The opinions
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