Author Archives: paulweeks2014

A root through plants 2

Lessons 2 and 3…

Having tried to establish that plants are, indeed, living organisms, it’s time to launch into experimental investigation time.

I display a range of plant material – garlic, mint, ginger, chilli, basil, rosemary… what have they got in common?

All nice in the kitchen for adding flavour to food. OK, fine, but why do these plants have this ability? They’re not making these tasty compounds for us, but for themselves. Why?

We circle back to the idea of how plants defend themselves, not just against predators, but also against infection.

I then ask them to design an investigation to test the anti-bacterial properties of various plant extracts. I used to provide this method…

Investigating the Antibacterial properties of plants UPDATED December 2017

…but I now much prefer, where possible, to let them design the experiment for themselves. Learn by doing. Learn by making mistakes. So I demonstrate the technique – extracting the compounds, soaking the discs, being aseptic – but let them decide on the approach. Most of them will forget a control disc, many won’t do repeats, they won’t all think of all the necessary control variables – but my feedback will highlight these basic omissions and they’ll do better next time….

This is motivating and interesting and different and they clearly enjoy it….

… and it’s a practical that really works. Garlic – particularly if you put it through a garlic crusher – inhibits bacteria to a spectacular extent, as they’ll discover in the next lesson, creating vast halos of inhibition around the paper discs. Homework is to finish their experimental write up and then design an advert for a garlic flavoured toothpaste.

Collecting the results doesn’t take much time, so it’s time to move things on.

So I ask them if they remember their babies, the little brassica seeds that they planted a week ago. We take a look. These Rapid Cycling Brassicas are not misnamed – one week is quite enough to see dramatic results. Oh look, I say disingenuously, one lot of plants went under the light bank, but this lot got left at the back of the lab. Tut tut, careless me, hem hem….

The difference is dramatic and the impact immediate. There are – I kid you not – audible coos and gasps when I do my big reveal.

I get them to make careful observational drawings of the difference between this “inadvertent” experiment. This is always a good exercise in forcing them to look closely and carefully at something. I also get them to list the controls and to think about the measurable differences between the two treatments.

They produce beautiful drawings and we discuss the differences. Plants under light bank have….

  • larger leaves
  • more leaves
  • thicker stems
  • purple stems
  • much taller stems
  • hairier leaves

We’ve controlled temperature and air and number of seeds per module and type of soil and volume of soil and availability of water and type and volume of fertiliser and species of plant.

Yep, the only difference is the light. Simple conclusion: light = growth. More light = more growth.

I’ve yet to come across any other demonstration or practical that so quickly and effectively gets this vital learning outcome across. I would choose this over and above all my other photosynthetic teaching resources.

But where to go next….? Find out next week!



A root through plants 1

Year 10 and plants is a graveyard slot tough gig at the Glasgow Empire at the best of times. Even bright, engaged, enthusiastic students will fail to engage with the topic and I have sometimes despaired at what can often seem like a pre-conceived rejection of everything to do with plants. Plants = Boring and there’s nothing you can do to change my mind!

As always, I keep refining, keep trying new ideas, keep looking for ways to excite their imagination and thence their interest. This might be an individual lesson, a new practical, a slightly different angle, and so on. But this year it has embraced the entire scheme of work, where I have gone back to what I consider to be the absolute basics.

  1. It has to tell a story
  2. It has to be an interesting story
  3. It has to be a story that makes sense, where the ideas and the concepts fall comfortably into the (hopefully!) receptive brains

Part of the problem, I suspect, is that too much of GCSE plant biology is abstract – the balanced equation, the various experiments which should be really fun and interesting but fail to find a a satisfactory context, all of which can leave students feeling confused, bored, disengaged.

So for the next 6 blogs or so, I’m going to take you through my new approach to teaching plants to Year 10. Lots of it is stuff I’ve done before – with a few new ideas thrown in, but it’s the over-arching theme that interests me and how it all flows from lesson to lesson.

Lesson 1

My usual introduction. I gather the class around me, pick a student who I know will be happy with what follows, and ask her to stand in a large cardboard box. It’s an unusual start to a lesson and amongst the giggles, there’s clearly curiosity. Where’s this leading?

I then ask the class if they’ve heard of the Mafia.

Yes, of course they have. We chat about Sicily, organised crime, gang loyalty, the rule of Omerta, and the punishments for anyone who breaks that rule. We agree that they are not nice people. For example, let us imagine that Izzi (in the cardboard box) has broken the rule of silence and an example needs to be set. We stand her in this box, fill the box with quick drying concrete, and then drop her off a remote bridge into very deep water.

This goes down very well and they are ghoulishly absorbed by the idea of a “cement shoe”. Except, I say, we’re feeling like a change, a more prolonged punishment. We’re not going to drop them into a lake. We are, instead, going to abandon them in the Serengeti. I let this sink in, and then ask, what sort of problems is Izzi going to face?

Predation is always the first suggestion. Yes, of course, all those lions and leopards and hyenas and vultures and so on. Why are they are a problem? Of course – she can’t run away and she has no protection.

OK, let’s give her a sub-machine gun to keep off all the things that want to eat her. What other problems will she face?

Food is generally next up. Yes, indeed, she can’t move around to find food. Still, never mind, let’s arrange for a sandwich delivery man to pass by once a day and give her a sandwich. And a bottle of water.

The point of the solutions is to a)keep the ideas flowing but also b)to show that she could survive with a few resources and a bit of ingenuity.

Once the immediate problems are suggested and overcome, I encourage them to start looking longer term. They realise, with much giggling, that if an attractive young man is deposited in the vicinity, also with a concrete block around his feet, friendship, romance, startingafamilyifitallgoeswellandtheydecideit’stherightthingtodohemhem is going to present another set of difficulties.

The brighter ones have already twigged where this may be heading, but I still ask the key question: what have I effectively turned this student into? They get it. A plant. The idea, of course, is that I’ve invited them to feel some empathy with a plant as a living organism faced with the same sort of problems any other organism faces.

Infuriatingly, despite the original and entertaining start, there is always some student who groans in despair and wails, “plants are so boring!!!” I control my temper and ask them sweetly to just give it a chance.

Anyway, boring or not, we’re off. We return to the problem of predation and discussing the kind of animals that predate plants – so not just cows and their ilk, but caterpillars, aphids, slugs, etc- and cover suitable defences – thorns, stings, spikes and chemicals. I show them these pictures of familiar plants up close and stress the biochemical ingenuity of plants, starting with the mechanism of sulphuric acid release from onion cells…

Trichomes and onion mechanism

I then put them into pairs and give them the name of a plant defence molecule. They have to find out the structure of the molecule, build it with molymods, and give a very brief presentation to the rest of the class about their molecule, which plant it comes from, and why it’s interesting. They really enjoy the challenge of building the molecules – some of which are fiendishly complicated – and the models give us a lovely lab display AND an important reference point for a future lesson. Stay tuned!

Plant secondary metabolite

I wrap up the lesson by getting them to plant lots of Rapid Cycling Brassica seeds, for reasons that will also unfold over the next few lessons….




So hormonal…

It’s time to introduce Year 10s to hormones.

But before I run you through my tried and trusted lesson for this, I need to issue a Health and Safety warning – namely, that virtually none of the following detail is on the iGCSE specification. What? Teach something that’s not on the specification???? Outrageous! This is the kind of dangerous bolshevik thinking that gets teachers a bad name… Shocking stuff.

Bear with me. I hope you’ll see why and how it works….

I start with this picture….

tanningWhat What are these two people trying to achieve?

OK, so that’s an easy one. They’re trying to get a tan.

By doing what?

By lying, scantily clad, in the sun.

So what’s this an example of? This interaction between sun and skin, what’s going on?

Straight off the back of their work on the Nervous System, they’re generally pretty quick to realise that we’re looking at a stimulus (UV rays) and a response (skin turns brown).

Can they suggest why is it unlikely to be a nervous response?

This can take a little longer, but the idea that skin goes brown slowly and gradually is obviously different to the rapid reflex actions they’ve been studying. Much comedy can be derived from imagining tanning as a reflex response. I’ll just go out in the sun – SPLAT – tan!

Right! Now move to this image.

body + pituitary

A human body.

And this???? the yellow dot?

body +

I love it when someone suggests it’s a brain. More chance for top class banter. Well, maybe your brain is that small, but generally brains fill skulls. Try again!

They usually don’t immediately know, so it’s then time for a quick game of Hangman, where I inevitably fail to break my losing run of 1,200 straight defeats, despite outrageous cheating, rule bending and general mayhem from yours truly.

Right – the pituitary gland! Let’s take a closer look…


And watch what it does…

The animation on my Powerpoint shows little blobs appearing in the pituitary and then moving out into the bloodstream.

The little blobs, I tell them, are a chemical called MSH, manufactured by the cells that make up the pituitary, which are secreted into the blood. And once it’s in the bloodstream, where’s it going?

Yes, everywhere!!! It’s all good Heart and Circulation revision from earlier in the year… With a little prompting they might even remember the part of the blood it’s dissolved in (blood plasma) and the name for these chemicals that travel in the blood (hormones).

Zoom back out to the body. Watch where this MSH molecule is going! And watch what happens when it gets there!

body + MSH

The animation shows it emerging from the pituitary, whizzing round the body, and arriving in the foot. And the foot then turning brown… In other words, it tans.

Huh? How does that work???

We need to look at what’s happening in the skin!



Here it is. A skin cell. And right behind it, another type of cell. With some recently arrived MSH in the top left corner.

What do they notice?

It’s pretty obvious. The cell behind the skin cell has little shapes on its membrane that, following their work on synapse mechanism, they can confidently call receptors. Which, they instantly see, the MSH can fit into.

It’s like I keep telling them – if you can do jigsaws, you can do Biology.

Let’s see what happens when the MSH fits into the receptor…

MSH in receptor


What’s that?

That is a molecule of the tanning chemical, stuff they’ve all heard of, melanin. And the cell that makes it is called a Melanocyte. Hence MSH – Melanocyte Stimulating Hormone.

Now watch….

melanin round nucleus

The animation then shows the melanin migrating from the Melanocyte to the skin cell and accumulating around… where?

So why would it do that?

We discuss the importance of protecting a cell’s nucleus, and the DNA within, from the mutagenic effects of UV rays…

And what happens if you fill more receptors with hormone?

Exactly. More melanin production.

OK, so that’s the mechanism. How is it modified by the sun?

Back to the pituitary!

Look what happens when its stimulated by light from the sun!!!

pit sun

Wow! LOTS more MSH…

…. which is duly taken all round the body in the blood….

…. and arrives at the skin.

Hmmmm. But skin only tans if it, too, is exposed to the sun. It can’t just be changes in the pituitary. So something must happen here too. What might that be?

They get it. The melanocyte responds by making more receptors!

And with so many more receptors filled with so much more MSH, what happens?


Bingo. Lots more melanin – in other words, a tan.

There is usually an avalanche of questions in this lesson. Partly to clarify things, but mainly to push for further answers. So you need to know your stuff – or just be very good a blagging. Either way, tt’s a great way of engaging students’ imagination and curiosity.

Tried and tested, this lesson works. It works really well. The combination of a clear narrative, simple but memorable animations, and a link to something they’re familiar with, is a winning combination. How can I be so confident? Well, 48 hours later, in the follow up lesson, they can recall every single detail – despite having not written a single thing down.

The full powerpoint, with notes and animations, is here…

Melanin production and hormonal control

They are also then ready to have a go at the follow up questions….

Hormonal Control of Tanning questions

Give it a go! Let me know what you think….




Bubble, bubble, toil and trouble…

When I’m starting off with a new class, and encouraging them to “have a go, because, after all, what’s the worst thing that can happen?”, I like to tell them about when I myself was in Year 10. My best subject of that year was History, and we had been studying the Renaissance and the Voyages of Discovery. As the end of topic test approached, I was vying with my best friend, Chris Mortimore, for top spot in the class (this was back in the days when class results were pinned to the classroom door for all to see). Lots of the available marks were for key dates, who did what to whom, or when did how to what, and so on…. I learned them all. Or nearly all.

When the final results were read out, Chris had beaten me to first place by one mark, because he had learned one date that I had not – 1517, the year when Martin Luther nailed his theses to the church door in Wittenberg and kicked off the Reformation. Nearly 40 years later, the only date I can remember from that year is the one I got wrong.

So my message is that getting things wrong is a really powerful way of learning. Don’t be scared of making a mistake – it will help you remember, it will help you learn.

It can also be a barrel load of fun, as my Year 10s found last week.

The context was Respiration, exploring this idea that living things need to release energy from food, and that while the reaction is chemically identical to combustion, the actual process must be slower and more controlled and take place at remarkably low temperatures, something made possible by the wonderful enzymes they learned all about in Year 9. I show them some yeast in a warm water bath, bubbling merrily away after the addition of some sugar. Look, I say happily, here’s an example of a living organism respiring sugar, using enzymes to do so, and producing carbon dioxide as a waste product.

They nod with varying degrees of enthusiasm and understanding.

But hang on, I say, how do you know that any of that is true?

They stop nodding and look puzzled. What do I mean?

Why take my word for it? I’ve just told you a whole load of stuff about what’s going on in that boiling tube – you’re just going to accept it on faith? What kind of scientists do you think you are?!?!?

They continue to look puzzled. Where is this going?

Go on, I say, design some experiments and test at least 3 of the statements I’ve made about respiration in yeast.

Both of my classes, Set 1 and Set 2, found this wonderfully difficult. Firstly, they struggled to grasp what I actually meant. I tell them to go back to the statement:

here’s an example of a living organism respiring sugar, using enzymes to do so, and producing carbon dioxide as a waste product

and think about how they could test the veracity of otherwise of what it says.

OK, they say, we could test the gas to see if it really is carbon dioxide….

Right! That’s the idea! Off you go!

Even on this easy starter for ten, there are some hilarious moments. The demo I showed them had a delivery tube passing bubbles through a test tube of tap water. Many of the groups let the gas bubble through the tap water and then attempted to collect the gas with a syringe, and then squirt the contents of the syringe through some lime water. When I suggest that they just move the delivery tube to a test tube full of lime water, they look at each other, and then laugh in mutual recognition of their own inability to see the simple and obvious. No matter – they won’t forget this experimental detail ever again.

I was also hugely amused by the group who tried to establish optimum temperatures of 37’C by heating the tube directly in the bunsen….

And then they really struggled. What else could they do? I tell them not to over-complicate. They have a very simple experimental set up – they only need to tweak the contents of the tube to test the other assumptions.

But what other assumptions????

And then, slowly, group by group, they started to see it.

What if we left out the sugar? What indeed! Try it!

They try it and, lo and behold, there is no bubbling. Seems that sugar is, indeed, vital for whatever is taking place in the boiling tube.

What next?

Well, there were, of course, some clues in the apparatus and reagents I had provided. Why the HCl and NaOH? Well, what effect would those chemicals have on conditions inside your boiling tube? Oh, pH change. Oh, enzymes. Oh…. oh!

Bingo, now they’re re-running the experiment but at high and/or low pH. And waddayaknow, the bubbling stops, or slows significantly. It seems reasonable to infer that some enzymes have been denatured.

The groups who had earlier tried to establish 37’C conditions in the blue flame of a roaring bunsen now realise that it gives another test – boiled yeast will be dead yeast. And dead yeast, it turns out, doesn’t bubble either.

What seems obvious to an experience scientist, or experienced teacher, was a really difficult thinking exercise for some very bright Year 10 students. But hard thinking is memorable thinking and without doing a single second of revision, or copied a single note from the board, the vast majority will have understood and remembered all the important points of the lesson.

Meet Smokey Pumba, the Forces Pig…

Visiting my mother in Cornwall over half term, she asked me to clear out some of the paperwork I had left filed in my old bedroom. I dutifully obliged and unearthed a treasure trove of documents, including letters from old girlfriends, my notes from undergraduate lectures with the incomparable Nick Davies, and my PGCE project work, including Section 1B (Subject Teaching), where I had to submit two essays based on my classroom work at one of my placement schools.

Here is the first one, submitted on Friday 4th June 1999 – blimey, where does the time go? –  titled: Teaching Forces: a critical evaluation of the use of a cartoon pig to enhance motivation and learning in a mixed ability Year 7 group. It’s not very profound or revolutionary, but it gives an insight into how I’ve always approached teaching.

nb: I’ve cut it fairly heavily….

Anyway, see what you think…


Traditional Forces teaching is characterised by line drawings of wheelbarrows and seesaws, stick-men and car braking distances, embellished with directional arrows to which are attached numbers, all suffixed with the letter N. Although some attempts have been made to make the concepts more immediately relevant and the illustrative examples more colourful, the subject, at a conceptual level, is inescapably dull. Children, especially Year 7 pupils, manifestly enjoy the practical work, playing with Newton meters, constructing pulley systems, and so on, but there is a discernible drop in enthusiasm when the making of paper ships stops, and the drawing of a wheelbarrow begins. It was during just such a lesson that I decided to introduce The Pig…

The Pig

(long section giving background describing girls disengagement from Science at secondary school).

The Pig and its use in the Module

I used a cartoon drawing of a Pig to replace the traditional abstract diagrams of weights. This proved immediately popular. Being a Year 7 class, our first priority was clearly the Pig’s name. Debate was fierce and ultimately resolved by a ballot of class suggestions that saw Smokey Bacon, Pumba and Pugsley emerge as the favourites. I rather liked the idea of the Pig being called after the Swahili word for “fart”, and the vote produced a tie between Smokey Bacon and Pumba, so we compromised and called it “Smokey Pumba”, a result, presumably, of eating too many bacon sandwiches. This important point established, the children effectively appropriated the Pig. It was their Pig and they cared about it.

The children liked drawing the Pig. They liked discussing what was happening to the Pig in certain situations (floating in a bath, standing on a diving board, stuck in a hole requiring a lever to extract him) and whenever I started a lesson with the words, “To explain this next idea, I need to draw the Pig…” the class would give a loud and spontaneous cheer.

pigs at the pool

The girls were concerned for its well-being. When I first drew a Pig to demonstrate the use of a Newton meter, I drew the supporting hook through the Pig’s back and a cry of dismay went around the class. When I subsequently marked the books, every single girl had very carefully drawn a little harness around the Pig’s tummy to which they could safely attach the hook. It was extremely touching.

newton pig

This involvement with the subject was also apparent during the lesson on Floating and Sinking. I merely sketched two Pigs in a swimming pool on the board, one with a greater downward Force than upward thrust (it was sinking), and one where the downward Force was balanced by the upward Thrust (it was floating). Again, the girls elaborated on the theme. Sinking pigs had unhappy expressions and were emitting a stream of bubbles as they sank. Floating pigs were cheerfully buoyant. In every case, the appropriate arrows and Forces were correctly drawn…

At the end of the Module, I set a homework which asked them to do a big drawing of a Pig (or Pigs) illustrating a scientific concept that they had learned that term. Cheerful pigs pushed supermarket trolleys to illustrate friction. Apprehensive pigs watched as the stopping distance of their car increased in wet conditions. Suitably attired astronaut pigs prepared for take-off in their rockets. And so on. If the enthusiasm and energy that went into this task was representative of their feeling for the course as a whole, then the Pig had done its job.

Forces pig

Case Study

Jessica was one of the most able pupils in the class. She consistently scored highly in homework and class-work and had done well in End of Module tests. Her contributions in class were alaso good. There was, however, an impression that she found it too easy and that she was under-performing relative to her ability…. She seized on the Pig as an opportunity to extend herself. She used her considerable skills as a cartoonist to create colourful and accurate Forces diagrams, and at the end of the course she produced a cartoon strip, that she had done in her own time, of Smokey Pumba stealing apples from an orchard (and its dire consequences!). The quality of her class-work and homework increased. She completed the End of Module test (and its extension) in 19 minutes flat and still came top of the class.


Analysing test results is a joyless task. The huge number of uncontrolled variables and the impossibility of doing matched pair comparisons render results largely meaningless, and besides, it is a depressingly narrow view of the purpose of education. I have therefore limited myself to asking two questions. Did the girls score higher than the boys in the test? And, more importantly, did the girls show a general improvement in their test scores relative to their previous results in other tests?

There was not a significant difference between the percentage scores of boys and girls (Mann Whitney test, N=13 boys, 13 girls, Z= -3.09, p>0.7). Girls did, however, score significantly better on their Forces test than they had on the previous two tests in the course (contingency table, 2DF, total chi-squared = 6.0734, p<0.05). In other words, girls showed a significant improvement in their relative score compared to boys….





Give me a beer…

Sometimes I just like to be silly.

Let me qualify that.

There are times, particularly when immersed in the complexities of metabolic pathways, that it really pays to do something different, to lighten the mood and provide another way of looking at something. Of course, you also want to provide something that helps the students understand a tricky concept, and if what you do is unusual and memorable, then it will also help them retain that understanding.

Here are my dramatis personae:

glycolysis elephant 1

Yes, you got that right. A purple cuddly elephant (a Xmas present from a tutor pupil), 2 juggling balls, an apple, a top hat and 3 dissection pins. Let’s see if the Biologists among you can figure out what I’m trying to illustrate. My students did!

So, first, I arranged the props as follows…

Glycolysis elephant 2

The elephant, lying on its back, with both juggling balls and one dissection pin, safely tucked between its legs. To one side and a little ahead, the apple with 2 dissection pins jabbed into it; on the other, also a little ahead, the top hat, brim up.

What am I trying to show?

At this point, of course, they haven’t a clue. But they’re already giggling. If nothing else, I have avoided that cardinal sin of teaching, being DULL.

I then slide the elephant along the table, making little dooby doo noises. More giggling. But I’ve got their attention! They really want to know what this is about.

When the elephant arrives between the apple and the hat, it becomes agitated! I switch from dooby doo noises to zips and zaps…

Glycolysis elephant 3

…things start to change! I take the dissection pin off the elephant and plunge it, with a pleasing “thunk”, into the apple. And I take one of the juggling balls off the elephant and put it in the hat. Note that the apple now has THREE dissection pins in it, which is the clue that enables them to guess the first clue…

Ah! Is that ATP???

Indeed it is. The molecule that acts as energy currency in cells, adenosine TRI-phosphate, with each dissection pin being a phosphate group. The apple with just two pins was ADP, adenosine DI-phosphate. By making a molecule of ATP, by transferring a phosphate from the elephant to the apple, we’ve manufactured some useful energy for the cell to use.

And making ATP this way is called…?

Substrate level phosphorylation…

Testing them without testing them, they get all the benefits of retrieval and application and usage, without the stress of doing something that scores them out of 10…

But what do the other things represent?

Let’s start with the elephant. It’s clearly (ahem) a…?

sugar phosphate

exactly, with how many carbons?


yes, the 3 carbon fragment that you get from splitting?

fructose bisphosphate

right, after the glucose has been?


well done, at the start of?


And the molecule we end up with? The elephant deprived of its dissection pin and juggling ball is?



So that’s the context and the pathway. They know all this, they’ve just not seen it represented with cuddly animals and edible fruit.

But now to the key bit…

What’s the juggling ball and what’s the top hat?

Again, they’re on top of this, now that the context is clear. The juggling ball represents hydrogen, stripped from the sugar phosphate by dehydrogenase enzymes, and the top hat represents NAD, the hydrogen carrier that is reduced when it receives the hydrogen from the sugar phosphate via the enzymes.

It’s worth stressing the importance of this. In order to convert sugar phosphate into pyruvate and make essential ATP, you also have to have an empty top hat.

But how do we empty the top hat so that we can keep doing this, and keep making ATP?

No problems here – they are all confident that the top hat delivers the juggling ball to the electron transfer chain in the mitochondrion, enabling it to come back and accept another juggling ball from the next elephant to pass by.

Trouble is, this only works in the presence of oxygen. What happens if there’s no oxygen? What happens if the top hat cannot pass on the juggling ball in this way?

Short answer, the whole thing stops. No more elephant conversion, no more triple pinned apples, no more energy for cell, in a word, death.


How else could we empty the hat? What else might be prepared to accept the juggling ball from the hat, freeing it up to go and help convert another elephant?

This takes them a little longer, but with a few nudges and winks and helpful joggling of the relevant prop, they get it…

The elephant!

Glycolysis elephant 4

Notice what we have here. We still have the triple pinned apple (the essential ATP), but we also have an empty hat because the juggling ball has been returned to the elephant.

(nb: what I really need here is another elephant to demonstrate that the process can continue…. note to self – buy more purple elephants)

But we don’t have pyruvate anymore. A purple elephant with one juggling ball (pyruvate) that accepts a juggling ball (hydrogen) from a top hat (NAD) has become a different molecule – a purple elephant with two juggling balls – or as biochemists like to call it, lactic acid.

The mystery of anaerobic respiration revealed, emphasizing the importance of oxidising NADH.

They liked this. They also liked this….

Hope you do too.

Whipping the Worm

Last November, I burbled on the IRIS project about curating the Human Whipworm Genome. A lot of genes have flowed across our screens since then, and as the project enters its second year I still have over 50 students from Years 10, 11, 12 and 13 enthusiastically learning about genome curation and putting it in to practice.

But this year I also want to start explore its potential for A-level teaching. See what you think…

Take a look at this screenshot from the Apollo genome editing software.

screenshot Apollo pic

Ooops. I work across 2 screens and I always forget that screenshots grab both of them.

OK, ignore the photo on the left, which shows my youngest son George in the process of diving into his snow burrow last winter. We need to focus on the image on the right. Let me try some judicial cropping…

screenshot Apollo pic

Ah! That’s more like it. So, what to look for?

First, notice how it’s divided into two vertical sections – the thinner one on the right with the heading “tracks” – we’ll come back to that. For now, concentrate on the left hand division. It has a few bars at the top, with zoom in/out icons and left right arrows, below that a yellow area with a long thing in it, and below that a thick white area with lots of horizontal parallel bars of  various colours and lengths.

First thing to notice, check out the numbers at the top of this left hand section.

5,000,000…… 10,000,000……15,000,000…. all the way up to 30,000,000…

These refer to the number of base pairs on the bit of whipworm genome we’re looking at. 30 million base pairs long!!!! This is a serious chunk of DNA! And if you look in the middle top, TTRE,chr2, it tells you we’re looking at the entire length of Chromosome 2 of the Whipworm. It’s there, on the screen, right in front of you, sequenced and accessible and real. Mind blowing.

I think this is an extraordinarily powerful image for conveying exactly what a genome is. But what makes it even more powerful is what you can then do with it.

Let’s change the view – we can do this by turning the various tracks in the right hand column on and off.

apollo screen grab

Now we’re looking at a chunk – a scaffold – of chromosome 1. Although chromosome 1 has been sequenced, the precise order of the sequenced sections has not yet been determined. So this is scaffold 1 of chromosome 1. Notice that it’s quite a bit shorter than chromosome 2, measuring just over 11,000,000 base pairs long.

I’ve zoomed in to create a view between 5,550,000 bp and 5,800,000 bp on the scaffold. I’ve selected tracks that just show the computer predictions of which parts of the genome look like genes. These are the things visible in the white area.

There is a huge amount of information about the nature of DNA in that image! When a student reaches the point where they fully understand it, they’re becoming reasonably fluent in the topic.

I’ve used lots of analogies down the years to try and help students understand the differences between DNA, genes, chromosomes and genomes. This picture illustrates all of this and more. So the 11,000,000 letters? That’s the DNA. A continuous strand, extraordinarily long, comprising an unbroken sequence of the 4 DNA letters. We can zoom in for a closer look…

genome zoomed in

Notice just how zoomed in we are… a span from 5,670,850 to 5,671,000, just 150 letters, and look!, you can see them! In the middle. That’s  DNA, sequenced, and on display, part of the genetic code that provides information for making Whipworms. The coloured bars above and below it, with their mysterious asterixes and highlighted letter Ms can wait for now, though I expect most of you can work out what they refer to…

Again, I just find this utterly amazing. The power of this software! And we’ll be using this zoomed in scale when we’re fine tuning our gene edits, but let’s go back to that other image.

apollo screen grab

Having established what DNA is, students can now readily see that a chromosome is just a very very long chunk of the stuff.

So what are the genes?

Well, again, there they are, the discreet horizontal line/bar combos in the white area (though it’s important to note at this stage that these are just the computer predictions as to which bits of the genome look like genes – sometimes the predictions are right, but all too often they’re wrong, to a greater or lesser degree, which is why the genome needs to be manually curated). But for now, let’s just take them at face value.

And let’s have a closer look at some…

apollo screen grab

Here are ten. Gene 1211 to Gene 1220. Notice that they correspond to the section of DNA directly above them on the genome – their position, or locus, on the chromosome. Notice that they vary in length – gene 1215 looks quite substantial, gene 1220 is diddy. Notice that they’re made up of coloured blobs connected by long, thin lines. Notice that there are overlaps between neighbouring genes. Notice that there are gaps. And notice that they each have an arrow at one end – for some, the arrow points to the right, for the others, the arrow points to the left.

This last observation illustrates another key point about DNA – being double stranded, the information, the code, the gene, could be on either strand. But the strands are anti-parallel, they run in opposite directions, so when curating the genes, you have to know whether they need to be read from left to right, or from right to left…

This year, I plan to get all of this in place with the Year 12s before we start looking at the actual structure of the molecule. How the students will then use the software to learn more about genes and what they do….

…. is a topic for another burble.

Watch this space!