Category Archives: Live chat highlights

Resource: Genetics CHAT transcript – Tuesday 3rd December 2019

Teachers: To ask your science questions, join the live CHAT with scientists every Tuesday 8-9pm.

Or ASK questions anytime on Genetics | Particle physics | Quantum physics

Moderator: To kick us off. As a challenge for you all, tell me one thing about Genetics you think I wont have heard about.

Reka – Industry geneticist: Did you know about ‘jumping genes’ (aka transposons), and how Barbara McClintock discovered them by studying colourful corn that had kernels of many different colours?

Eugene – Wellcome Sanger Research Fellow Did my PhD studying human transposons

Francesca – Wellcome Genome Campus Education Development Lead: @Eugene @Reka what is the function of a Transposon?

Nikolai – Plant geneticist: Transposons can be fab. Transposons offer a way for genomes to evolve by copying existing genes (fully or partially); these copies are then freed from evolutionary constraints and can obtain new functions (yay) or simply become a pseudogene (booh)

Reka: @Francesca Tough to say as far as I’m aware – they are remnants of viruses that have embedded themselves in our genomes. I believe one theory is that while sometimes they can insert themselves into a gene and wreak havoc, they also contribute to maintaining genetic diversity

Eugene: The function of themselves as a genomic parasite is to make more copies of themselves — i.e. to reproduce. But like @Nikolai and @Reka say they can be coopted to do cool stuff to the genome.

Francesca: @all Thanks, how are scientists using transposons in research? It might be nice to give teachers some examples

Moderator: I’m going to ask really basically here, is a transposon then just a section of the DNA?

Eugene: Yup it’s a piece of DNA that can move around the genome. They can be used for a bunch of stuff. Early genetics studies used them to randomly mutate the genome and observe organisms for “strange” phenotypes.

Nikolai: @Francesca Classic examples of using transposons in research is transposon tagging and enhancer traps, which ultimately helped to identify many genes in maize (the species where transposons were discovered in)

Francesca: @Nikolai so they flourescently labelled the genes to see how they moved around?

Nikolai: No fluorescent tagging; that is too high tech 🙂 Essentially, you “move” a transposon close to a gene. In most cases nothing will happen, but in some lines a phenotype change will occur. Standard forward genetics screens were then used to identify the DNA sequence that led to this change (i.e. a gene tagged by a tranposon)

Moderator: When we say early research, how far back are we talking? Manipulting the genome feels very recent…

Eugene: I want to say greater than 25 yrs ago but could be longer. We’ve been editing the genome for a long time! It’s just a lot easier now with CRISPR

Nikolai: Genome manipulation is old. Essentially all of domestication is a story of genome manipulation (cows, dogs, wheat, rice,etc). But our tools are now much better to do this.
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Francesca: @all Who uses CRISPR here?

Nikolai: *holds up hand*

Francesca: What do you use it or and how does it work?

Nikolai: I use CRISPR in my research to study the function of a gene. Specifically, I am looking at sequences within the gene that control how it is “expressed”, i.e. when and where it is switched on.

CRISPR/Cas9 is a combination of two elements: one acts as a homing device (i.e. it identifies a unique piece of DNA sequence within the genome) while the other is a set of molecular scissors. In this manner, you can cut DNA in a single unique place. This cut is repaired but sometimes errors occur. It is these errors that you look for, as these will change the function of a gene.

Francesca: What are peoples thoughts on the use of CRISPR to edit the twins in China?

Reka: Scientifically it’s super cool, ethically it’s super not cool. There have been few details about it, and the scientist who did it has been AWOL for some months – just today actually I read that bits of the publications he wrote [but which never got published] have been revealed today.

Nikolai: Editing those twins was unethical (parents were not aware of what was going on) and pretty pointless. The knowledge behind the gene and its effects on disease resistance is not great afaik.

Moderator: I heard it wasn’t really gene editing or something is that right… if so what was it?

Nikolai: At the moment CRISPR/Cas9 is not true genome editing, but simply a tool to delete short stretches of DNA. The twins were “treated” with a CRISPR/Cas9 approach, i.e. a chunk of DNA in a particular gene deleted. This is not true editing, as it can only work in one direction (no “undo” button). But you could couple a different tool to the homing device, e.g. a deaminase that essentially creates a G-A mutation (a single base pair mutation).

Moderator: So it was like an audio editing tool with only one function, delete, trash etc

Nikolai: Yes, only one function. But this field is moving on (at different pace in different species). Ultimately, we should be able to replace any sequence within a genome with any other sequene, i.e. repair faulty genes (cystic fibrosis).
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Moderator: Has anyone done any outreach or engagement work recently with schools? If so, what is it that students find interesting about you and your work? How do they connect with you?

Eugene:  I was actually at a school this past Friday talking with students/teachers about genetics. Interesting to hear their takes, they really find it fascinating that so many things have a genetic component.

Francesca: At the Campus we have a visits programmes where schools can come to us and an outreach programme where we can go out to schools. Students really enjoy finding out about the latest sequencing technology – the MinION , the portable DNA sequencer gets them very excited. We have actually taken it into schools and done live sequencing!

Moderator: Woah, what do you sequence? The teacher?

Eugene: XD That would be great!

Francesca: We took in a cleaned up sample of bacterial DNA and they were able to tell within 30 minutes what species it was. Very Cool!

Moderator: Fascinating that can be done in class. Ok, what’s a way to for teachers to give students that sort of wow moment about genetics, maybe with less tech 🙂

Francesca: One of my favourite activities is a really simple one – DNA extraction from fruit using households materials like washing up liquid, salt, water and Vodka (has to be really cold). We have a cute animation on yourgenome and instructions.

If teachers are worried about using Vodka, rubbing alcohol / Isopropynol works really well and doesn’t need to be cold.

Reka: I love that one, it’s also my go-to example 🙂

Francesca: We also have Investigate activity resources which looks at genetic variation such as bitter taste, smells, ear wax type etc. PTC strips are great, some people are so surprised when they can taste something and others can’t. We have also just worked with the BSA to create a set of CREST superstar awards for 7-11 year olds to get them thinking about DNA and the world around them.

Nikolai: A nice “low tech” example of genetics are the glass gem corn varieties; these maize lines produce cobs with colourful kernels. It was with these that Barbara McClintock discovered tranpsosons (can’t get rid of them tonight :))

Reka: Nope, they keep jumping right back into the conversation!
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Moderator: Change of track, did anyone see the documentary from BBC4 recently about eugenics, Science’s Greatest Scandal? Talk about eye opening. How much day to day do you get time to think about the ethics of your science?

Eugene: I’ve been thinking a lot about it lately, I work around the Genetics of Intelligence, and it is a very heated topic. I’ve been thinking a lot about how to properly communicate my science and make sure that what I am doing is well controlled and tested.

Nikolai: Haven’t seen that documentary (yet). I think the Kurzgesagt Youtube channel had a good video on Eugenics.

Reka: Kurzgesagt is a fantastic YouTube channel! Educational and gorgeously-drawn/animated. That could actually be a really nice resource for teachers too!

Francesca: They are good, may be a bit long for some students but completely agree they are FAB! @Eugene, tells us about the polygenic risk you have been working on its really interesting.

Eugene: So what we are trying to look at is how “risk” for developmental disorders may be inherited from parents via polygenic scores.

Moderator: @Eugene how would you use a polygenic score once you have one?

Eugene: Depends at the moment on which score. For psychological traits, it’s kind of a fun thing to see how it compares to my actual trait. For something that could be actionable, like my risk of prostate cancer, I would probably try to be healthier and go to increased screening. So it’s very variable on which “score” you are looking at.

Francesca: What is the simplest way to explain a polygenic score?

Eugene: I think the easiest way to explain is that each of us have pieces of our genome different from other people, and that those pieces can increase or decrease or risk of a certain trait. If we add all of these pieces up, we can get a score.

Moderator: Whats the score out of? Trying to picture it

Eugene: In terms of a scale of 1-100? It doesn’t really work like that. It’s like a bell curve.

Nikolai: Yes, variability!! Whatever your genetics, the environment has a key role and can modify or even override it. It’s both the saddest part of being a geneticist (booh, what happened to my mutant) and the most exciting (new functions!).

Eugene: Most people are at the average, and some people are at the extremes. And those people at the extremes have higher/lower risk

Reka: It’s usually calculated not just for one person but for a whole bunch of people – for example all 500,000 UK Biobank participants. You then look at the distribution of those people’s scores for a given trait/disease, and compare any ‘new’ people’s scores to these to see where they are on the scale.

Moderator: I wonder, is the using the word ‘risk’, err risky, in some contexts, cos of its negative connotations?

Eugene: Yeah, the field has started to move away from “Risk”. For things like height, its now just a polygenic score, but for medical stuff it can still be a polygenic risk score. Subtle, but important.

Moderator: Ok so this is something that might be used in clinical settings or is it already being used?

Eugene: Not quite yet. NHS is working on evaluating clinical utility. It is my opinion (and many others) that they will enter the clinic at some point in the future.
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Posted on December 5, 2019 in Live chat highlights, News | 1 Comment

Resource: Particle Physics CHAT highlights – November 2019

Teachers: To ask your science questions, join the live CHAT with scientists every Tuesday 8-9pm.

Or ASK questions anytime on Genetics | Particle physics | Quantum physics

Moderator: To kick off, I challenge you to tell me one thing related to particle physics I wont know, or at least will not have heard much about in the news.

Scott – STFC physicist: I have a fact that I learnt the other day. I’ve always known how screamingly, horrifically strong the radiation is coming off our target, but I recently learnt that it’s about a thousand times stronger than that! Like: serious melt your face off insta-death levels (if unshielded). Thankfully our radiation shielding is perfect and the dose rates are below background just outside the shielding. It’s actually safer to stand next to it than to live in Cornwall or Glasgow with lots of granite bedrock!

Moderator: Why is the target so radioactive? Whats it made of?

Scott: We’re smashing very powerful and relativistic proton beam into a tunsten target to generate neutrons for materials science. Neutrons are fairly nasty at the best of times… and those are the things we want to make! The tungsten also undergoes all kinds of other nuclear processes. Ergo Gamma-rays and prompt fission products.

Moderator: “Seriously melt your face off insta-death levels?” I’m wondering if that is an official SI unit reading?

Scott: If you want a proper unit: it’s 200,000 Sieverts. One Sv is guaranteed quick death, so hundreds of thousands more is utterly terrifying.

Moderator: Yeah, insta-death level will do nicely.

Lucy: I think it is much easier to understand than Sieverts
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Meirin – CERN physicist: Hi, I prepare CERN data for use in educating students of about 16 years and older

Teacher: Hello everyone! Thanks for the introductions. I’m a high school physics teacher – this is my first fully qualified year and I am teaching up to advanced higher level. @Meirin what sort of data are you preparing for students?

Meirin: Data to teach students about particle physics but also about transferable skills like programming and data analysis

Teacher: Is that something that will be publicly available? I’d be keen to get my classes involved. Our school doesn’t have great IT at the moment but we will soon be getting iPads for all pupils

Meirin: Yes it’s all on !

Teacher: I haven’t looked at the website in much detail yet, but what sort of activities would be possible using the data?

Meirin: The “get started” section teaches how histograms are used in particle physics by searching for the Higgs boson decaying to W bosons. The “web analysis” section introduces how programming is used in particle physics by measuring properties of particles such as the Z-boson. The “Data & tools” allows download of all available data to do some proper programming projects to e.g. search for Beyond Standard Model particles

Teacher: Thanks. Time permitting I’d love my pupils to use some real particle physics data rather than just answering textbook questions. Pupils can also struggle to understand what a career in particle physics might look like so using real data from ATLAS would help with that too

Meirin: Honestly it’s such a good introduction to research. I did my masters on ATLAS Open Data so wouldn’t be here without!

Teacher: That’s really good to know, it will be really helpful to tell my pupils that.
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Teacher: I’m interested to hear the routes you each took into your current career? My pupils definitely don’t appreciate the wide range of opportunities that studying sciences can provide

Scott – STFC physicist: I studied undergrad astrophysics at Uni. After that got a job on STFC’s graduate scheme on a completely different subject: accelerators. Been here ever since and am now group leader

Susan – Neutrino physicist: Did Astronomy and Natural Philosophy (as they still called it then) at Glasgow. Then PhD (also with Glasgow) working at DESY in Hamburg. Then postdoc with Rutherford Lab, also based at DESY, followed by postdoc at SLAC in California, before landing lecturer post at Sheffield

Savannah – CERN physicist: I didn’t know what I wanted to do for ages but always enjoyed maths and science so did these subjects at school. I then studied physics at Manchester University (integrated master’s) and now I’m doing a PhD there too 🙂

Edoardo – Theoretical physicist: I liked scientific subjects at high school and then got into physics at university. In the last year I went for theoretical topics.

Anne – Dark matter physicist: I really enjoyed (and was good at) maths at school, but wanted to apply it to something interesting rather than doing maths for maths sake. And I discovered cosmology via popular science books and documentaries. I then did Physics at Oxford followed by a PhD in early Universe cosmology at Sussex.
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Teacher: What would you say the easiest way to show what you do to school age children would be?

Lucy – Particle physicist: I spend my days doing programming and maths/algebra! But we always try to work with pictures/videos and something hands-on to get students thinking. We have an exhibit with a galton board containing a hidden shape (which changes the way the balls fall through and hence the pattern at the bottom) and computer programmes that simulate this.

You have to try different shapes until you find the one that gives a similar result to the real experiment. This is similar to how we understand particle physics experiments – we build a computer model of them and predict what we think we will see as the outcome. Then compare that to the experimental results. Since with particle physics we can’t see what is happening when e.g. two protons collide but we can get a measurable outcome (electrons, photons, quarks/gluons and their directions and energies)

Teacher: So are you getting to build the computer models? The shape things is like a simple thing we have in the cupboard actually, different weighted tins, I could try them with the pupils for a variation on that

Lucy: I don’t personally build them, but I am working on calculations that will (hopefully!) help improve them. Many others in my research group do work on the programmes used to understand CERN’s results from the LHC

Teacher: So photons, quarks and gluons – when describing protons, electrons and neutrons we basically speak about mass, where they are and what their charge is – where would they fit into this model for me and my pupils

Lucy: photos have no mass and are the particles of light – so a beam of light is many many photons. Quarks and gluons are what you find if you break apart protons and neutrons. On the most basic level protons and neutrons are made of three quarks each, and gluons are the “glue” that holds them together (they are a force particle like photons)

Teacher: So would the quarks be equal in size?

Lucy: Quarks have an electric charge of either 2/3 or -1/3 (there are two types) and gluons have no electric charge, neither do photons

Teacher: What are the quarks doing? Is it like a polymer unit type thing where they are all needed to carry out the role of protons having a positive charge and neutrons having a neutral charge or is that too simplified?

Lucy: Sort of yes, in that a proton “gets” its charge from the quarks within it, and a neutron contains charged quarks but is overall neutral. It’s similar to breaking an atom down into electrons, protons and neutrons – quarks and gluons are the “insides” of the protons and neutrons

Teacher: Would you then find quarks and gluons isolated anywhere or can you only find them when you blast the neutrons and protons apart?

Lucy: You can’t find them isolated! Quarks are always in at least pairs (known as mesons), or in threes like the protons/neutrons. You can also get more quarks bonded together but these have only been seen at the LHC. And wherever there are quarks there are gluons holding them together 🙂 Gluons carry what’s known as the strong force – which is much stronger than the other forces like electromagnetism. And it’s partly because it’s so strong that you don’t find the particles alone

Teacher: So what type of a substance are gluons made from? like biological enzymes where they have a specific shape relating to the quark or like a bond in chemistry?

Lucy: Gluons are made of gluons if that makes any sense? They can’t be broken down (as far as we know). They are like a bond in chemistry (which works between two differently electrically charged particles, and the bond is made of photons), so gluons are the bonding between quarks
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Teacher: What one thing do you think is the most important thing about stars and planets which school kids should learn – there is so much information and limited time

Scott – STFC physicist: I think it’s important to understand just how mind-bogglingly huge space is. It takes days just to get to the moon. There is enough space between us and the moon to fit all the other planets in. And that’s just the moon! Saturn, for example, is over a billion miles away

There’s such a lot of nothing in space that it’s mind-boggling. We’re brought up seeing the Millenium Falcon dodging asteroids, when in reality you would fly through the asteroid belt on your way to Jupiter and not even see anything out the window!

This website is an excellent demonstration of the scale of things. Really accessible and puts everything into perspective:

Especially useful for kids used to scrolling endlessly on their smartphones: now they can scroll endlessly through space! 🙂

Teacher: Ha ha excellent!
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Posted on December 3, 2019 in Live chat highlights, News | Comments Off on Resource: Particle Physics CHAT highlights – November 2019