Monthly Archives: January 2016

Hooked on Hooke and other thoughts

I tried something new this week with Year 13 Photosynthesis. Instead of giving them a brief introductory overview of the process, I challenged them to figure it out for themselves, using the observation that it’s Respiration in reverse. Simple idea, but it worked really well. They started by going for the trees rather than the wood, trying to remember all the intermediate compounds and exactly what happens in the Krebs’ Cycle. But after a hint to ignore the specifics and focus instead on the general principles, they put it all together. Since Respiration finishes with oxygen accepting hydrogen to form water, Photosynthesis must start with water being split to form oxygen and hydrogen. Oh, says one of my brightest students, is that what they need the sunlight for?

From there, they decided there must be a hydrogen carrier… but to do what? What do hydrogen carriers do? They end up reducing other things. But what? Well, what’s the other waste product in respiration? Oh, is the hydrogen added to the carbon dioxide? Bingo! So what happens to the carbon dioxide? Oh, it’s being reduced. To form? Carbohydrate.

They felt very pleased with themselves so had some fun deriving the absorbance spectrum for geranium leaf photopigments.

abs spectra

Nice, quick, easy practical – yet another use for colorimeters – with some gentle questions for homework. Just left time to read the Carbon chapter from Primo Levi’s Periodic Table – which makes for a glorious introduction to this topic. I always feel that students’ negative reaction to plants is just a failure of imagination – Levi’s carbon atom fantasy tries to counter this.

Meanwhile, the introduction to Cells with Year 7 is going down well. I really like recreating scientific breakthroughs of the past – apart from anything else, it allows you to tell your students that they’ve just emulated a genius – so getting them to slice cork and make a detailed drawing of what they observe sets things up nicely. I accompany this with a reading of Cops and Robbers (Janet and Allan Ahlberg) for this priceless page

DSC_8854

“Here are the robbers of London town

In cells all gloomy and grim.

“Let us out! Let us out!

Not guilty!” they shout,

And, “It wasn’t me – it was him!”

 

which absolutely nails the concept of why he called them Cells. And then they build little models of the cells and use their homework to write a letter from Hooke to a friend about his exciting new toy. They love ageing the letters with tea, burning or tearing the edges, using a wax seal, and so on. This year, I combined their letters with their cell wall models to make this display.

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Note the Year 12 protein model dangling in the foreground….

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Your modelling career…

Last week I burbled briefly on Genetic Drift and said I would return to Hardy Weinberg in a future post. Well, here it is… (in a curious case of deja vu, part of me is convinced I’ve already written about this, but can find no evidence! if you’ve read this before, just put it down to advancing senility…).

I think most students find Hardy Weinberg difficult. It’s abstract, it’s got an equation that just seems circular and self-referencing, and it’s hard for teachers to avoid a chalk and talk approach followed by lots of practice of number crunching.

There are some super resources to help with this and I reckon you could usefully get your class to teach themselves the entire topic from this Pearson LabBench Activity.

But, as you know, I like my lessons to involve students doing things, and especially I like making them think. So I came up with this lesson plan.

First, the Powerpoint. What’s wrong with this woman?

Allele frequency intro

Of course, they can’t tell there’s anything wrong just by looking, though they come up with some very creative guesses.

The only clue is in her ethnic origin. Usually, at this point, someone gets sickle cell anaemia. Time out to talk about sickle cell anaemia, why it is a bad thing, and how it is inherited. A picture of a normal vs sickled cell, and then a heterozygote genotype.

The next slide shows a population – stress population – of individuals of varying genotypes. But we’re not going to count individuals, we’re going to count alleles.

The slide helpfully separates them to aid this. I get them to count the HbN alleles, and right at the start it’s worth pointing out the basic principle that they don’t then have to count the HbS alleles – if they know one, they know the other!

We then work out frequency. Easy, isn’t it? Again, look, if you know one, you don’t have to work out the other – they have to add up to 1.

Back to the population. What about the next generation? Are all of those individuals going to pass on their alleles? Why not? We quietly vanish the HbSHbS genotype. What’s the effect on the respective allele frequency?

So, there’s the setting. We’re looking at allele frequency in populations.

Now it’s time to start the modelling. The sheet…

Modelling Allele Frequency in Populations

introduces them to HardyWeinberg without any attempt to explain or use the equation. That can come later. For now, we’re interested in this assumption that allele frequency doesn’t change (you can demonstrate this quite nicely with a pack of cards dealt into pairs, picked up and shuffled, and re-dealt). The exercise mentions the assumptions required, and describes 3 of them. The idea of the exercise is for them to identify 4 more.

The rest is fairly self-explanatory. They divide into pairs, count out some coloured beads, and play around with them as per the instructions. You could talk a little bit about why this kind of thing can only be done as model, rather than an experiment. But they get practice in counting model alleles and working out frequency so they become very comfortable with the process.

The bit they will find difficult is imagining what events these might represent in real life. But with a bit of discussion, a bit of prompting, they figure it out. So for the first event, what could cause half your population (with their alleles!) to disappear overnight? For the second event, what can you say about the blue allele? Why aren’t those alleles being passed on? The third and fourth are more straightforward, though it helps to stress the correct terminology.

And you can then have a discussion about how realistic HW is and when/why you might find allele frequencies changing at a higher rate. This exercise …

Changes in Allele Frequency in real life

gives a few ideas.

I also wasn’t aware until recently that HardyWeinberg assumptions can be used to assess the accuracy of DNA sampling in a population. The slides here show the results of two genotypic assaying samples. You want to check whether they are valid samples. So you compare the numbers given to the Hardy Weinberg equilibrium. What does this tell you about the two samples?

HW assay

That’s enough for now. We’re being inspected and I think that’s someone at the door of the lab….

ASE was ACE

One spin off from the BTOY award was being invited to chair a series of talks on Biology in the Real World at this year’s ASE conference in Birmingham. It was my first time at this event and it was brilliant. Indeed, I’ll be back next year, if I can wangle the time off, as I was only there for the day and didn’t have nearly enough time to explore everything that was going on. But the overall effect was energising, exciting, inspiring – I came back to Oxford buzzing with new ideas and a bag bursting at the seams with bumpf. Many thanks to the Royal Society of Biology for the invite…

The talks were brilliant – here’s the briefest of summaries….

  1. Professor Joanna Verran (Manchester Uni) on Biofilms. Amazing images of e.g. 1000s of bacterial cells on a single grain of sand
    1. www.erc.montana.edu/CBE
    2. https://student.societyforscience.org/articles/slime-cities
    3. I, SuperOrganism – popular book on human body’s biofilms
    4. Fascinating stuff on quorum sensing and possible role in bacterial control
    5. 99% of planet’s bacteria live in biofilm communities.

 

  1. Dr Charles Lane (FERA and SAPS) on Killer Plant Diseases.
    1. Great practical on SAPS website on how to demonstrate Koch’s postulates with rotten apples
    2. Ash dieback first plant disease to be discussed in COBRA meeting

     

    3. Professor Saffron Whitehead (Society of Endocrinology) on Hormones and Homeostasis

    1. Steroids highly conserved – found across Animal Kingdom
    2. Ketoacidosis only occurs in Type 1 Diabetes (because ketone body production inhibited by insulin)
    3. Glycosylated haemoglobin main problem from diabetes leading to similar complications of CVD

4. Professor Greg Hurst (University of Liverpool) on Microbial Partners

  1. e.g. 10-20% of human calorific intake from bacterial digestion in gut (short chain fatty acids – acetate, propionate, butyrate)antibiotics bad for cows/horses because e.g. horses get 80% plus of calories from bacterial digestion. aphids have specialised organ for cultivating symbiotic bacteria that make essential amino acids lacking in phloem – 200 million year old symbiosis. desert rats eat leaves of creosote bush – only because their bacteria detoxify the creosote – a desert rat on antibiotics becomes sensitive to creosote
  2. breast mile contains complex polysaccharides specifically to encourage growth of particular bacteria
  3. aphids not found in tropics because bacteria temperature sensitive
  4. insects dependent on blood/phloem become sterile if fed antibiotics – because they rely on bacteria to produce vital nutrients otherwise lacking in diet
  5. apologising for breaking wind is taking responsibility for the microbial part of you, as methane/hydrogen sulphide are only produced by bacterial enzymes
  6. Review of idea of Holiobionts and how organisms can borrow skills from other Kingdoms by forming a symbiosis/symbiosis opens up new ways of life/niches

5. Dr Ginny Acha (Association of the British Pharmaceutical Industry & British Pharmacological Society) on Personalised Medicines

  1. Interesting data on efficacy of drugs – numbers show percentage of patients who do not respond to drugs for that condition
  • Anti-depressants 38%
  • Diabetes 40%
  • Arthritis 50%
  • Alzheimers 70%
  • Cancer 75%
  • Nice review of history of understanding of blood cancer and how increasing understanding has led to more effective treatment
  • 100 years ago – “disease of blood” – 100% mortality
  • 80 years ago – leukaemia vs lymphoma
  • 60 years ago – 3 types of leukaemia and 2 types of lymphoma
  • Today – too many classifications to note down! 70% survival

Back at school and a lovely lesson with my Year 13s, exploring Genetic Drift through retinitis pigmentosa on Tristan da Cunha (use Google Earth to dramatically show the geographic isolation of this volcanic island)and a rather splendid colour worm game, followed by allele frequency and selection with sickle cell anaemia Sickle Cell Anaemia change in allele freq.

I came up with the idea of applying rates of mutation through Sean B Carroll’s excellent The Making of the Fittest where he does the same with colour vision in birds (brilliant chapter!). It works quite well but, boy, do they struggle with calculating the probabilities! How do you get on?

One way to help is to rephrase the problem. If the rate of mutation was 1 base in 3,000,000,000, what would be the probability of any one person having that mutation? So if the rate is 175 in 3,000,000,000….? And so on. Of course, a point mutation will only have an effect if it’s the right point mutation…. so what do you have to do to the probability?

I send them off to do some homework on Eugenics and applying Hardy Weinberg to the elimination of cystic fibrosis by selective breeding eugenics worksheet with Hardy Weinberg. Yields dramatic results!

I’ll say a bit more about Hardy Weinberg next week, as it’s a nice example of how to make what appears to be dry and theoretical into a hands on, student led learning activity.

But there’s also an Inspection next week, so if it seems a bit rushed, you’ll know why!

Sex with Year 13

Happy New Year! I hope you all had a super winter break and have started the Spring term energised and invigorated.

I’ve come back to a department where half the tubes of fruit flies in our breeding experiments have been desiccated into little wispy fragments after being left on the light bank. I also tracked down the missing department hamster – trapped in a cupboard, she was considerably thinner, drier, flatter and deader than when I last saw her. I am surprised by how upset I am – she was a particularly lovely and beautiful hamster.

Anyway, I thought I’d kick off 2016 with an idea I had from the superb Life Ascending by the incomparable Nick Lane. It’s a way of introducing a topic that aims to be memorable by challenging students to look at something in a completely different light. It’s also a desperate ploy to try and increase my WordPress stats, for that topic is Sex (sorry, lonely person in Russia, you’re going to be disappointed again).

Now, for most teenagers, indeed, for most people, the word Sex means something very specific. I remember a student who was distinctly sceptical at the notion that plants were actually living things, but absolutely categorically refused to believe that plants have sex. No, no, absolutely not. For her, sex meant something very specific that was certainly an activity that plants could not possibly partake in. Nothing could shake her belief in this. I like to think she would have found this lesson interesting….

So without mentioning the word Sex, I start with this interactive powerpoint.

Introduction to Sex

Go on, open it up and have a go. Actually, it’s not very interactive. All they do is choose a colour, you click on the box and it reveals a picture. Click on the picture and it takes you back to the first slide (apart from two, which are hyperlinked to video clips). As you explore the pictures and videos, just ask the class, do each of these examples make the world a richer place?

There are some surprising responses. One class was absolutely spellbound by the Marriage of Figaro clip and my frenetic attempt to describe the plot (note that it doesn’t have to be Marriage of Figaro – London Burning by the Clash would be just as good, or even, god forbid, One Direction….) but claimed to be completely disinterested in fashion. Another class agreed that flowers were nice but didn’t think much of butterflies.

But everyone loves the Birds of Paradise, David Attenborough, dancing and Van Gogh. Phew!

So then the question is, what do they all have in common?

The answer, of course, is Sex. And it’s fun to discuss all the various reasons. But the point I hope they take away is Nick Lane’s point, that an Earth where Sex had not evolved would be a dull, grey, monotonous kind of place. Whatever Sex might mean for them on a personal basis, it has more profound implications than our human-centric view of it.

Not sure they were entirely convinced but it was different enough for me to give it another go next year (if nothing else, it ticks the unpredictable/variety boxes of lesson planning!).

I then like to approach the topic from the theoretical challenge of why on earth Sex ever evolved in the first place. There’s a wonderful 10 minute sequence at the start of Frozen Planet where a male polar bear looks for a mate. Not only does it look amazing, but it graphically illustrates the problems with Sex as a method of reproduction, starting with the camera panning back to reveal the poor solitary male in a vast empty wilderness. All that time and energy looking for a mate! Surely it’s much easier and simpler and quicker to bud a new polar bear from your shoulder….

By the end of the clip, the male is absolutely battered, limping, shattered, covered in blood, from fending off so many rivals. It’s real Iorek Byrnison/Iofur Raknison stuff. Clearly, this is a seriously risky business! It just doesn’t make any sense. I shower them with questions. Why else is it risky? Childbirth. Being eaten by your mate (some species). STDs. How else is it costly? Display. Song. Growing special “come hither” feathers. I tell them about the male skylarks who fly vertically upwards while singing their hearts out. It might be beautiful, but he’s only doing in a desperate attempt to have Sex.

And why else is it just plain daft, when you could just clone yourself?

With a little prompting, they see the idiocy of diluting your perfectly good genome with some dodgy genes that you have no idea where they’ve been are probably harbouring some potentially lethal alleles. And why dilute it by 50% anyway? Don’t you want your children to be 100% related to you? Sex? Utter madness!

They tentatively point out that Sex generates variation.

Aha. That’s true, so it must convey some pretty major benefits to outweigh the negatives

So then I tell the story of the New Zealand snails. They really like this, as they like most stories (never underestimate the power of stories – it’s how they remember). It’s important to use the Powerpoint as a prompt for questions.

New Zealand Snails and sex

Where’s this? They usually get New Zealand, though other answers are generally entertaining.

Where’s this? Big river estuary. Yes, it’s the Thames. Deptford. I once had a girlfriend in Deptford. Had to get the 107 bus from Euston to visit her. But I digress.

150 years ago, how would you get from London to New Zealand?

Why would you want to?

I talk about Eric Newby’s The Last Grain Race and his hilarious recruitment on to a Scandanavian wheat clipper (worth reading just for the “oop! Ooop!” bit).

Which way would you go? Why would it be a bad idea to hug the coast of Africa? Tales of the doldrums and yellow fever and the trade winds.

And so, you reach New Zealand with your sheep and off load them. But what do you need to do before you can go home? Yes, this is before you could have filled your hold with crates of Marlborough Sauvignon Blanc, so you need some ballast! Take on some rocks from the fresh water estuary…

…. oh, look, there’s a stowaway…

Back to England! Which way? Yes, don’t fight those prevailing winds in the great Southern Ocean.

And back in Deptford, ready to take on more sheep, what do you do? Yep, unload the ballast and off hop the snails. Who happily go forth and multiply in this exciting new land…

And finally you can get to the whole point of this long winded story!

Because snails have the option. Asexual or Sexual reproduction. They can do both. And in New Zealand, they have Sex. And in England, they don’t.

Why???????????

You’re all bright enough to figure this out for yourselves, if you don’t already know, so with the general advice that if you come back as a freshwater snail, make sure you’re in New Zealand, that’s enough for this week.