Monthly Archives: June 2011

Whose right to life?

We in S104 have all been assigned a primate species to research. We are then to have a discussion and decide which of the primate species we would prioritise for conservation, and why.

The species are: Pongo abelii (the Sumatran orangutan); Colobus angolensis (the Angola colobus); Leontopithecus rosalia (the golden lion tamarin); Eulemur coronatus (the crowned lemur); and Tarsius dentatus (Dian’s tarsier).

I’m not sure yet which species I would prioritise for conservation, but the discussion on the tutor group forum has raised some interesting points – scientific and philosophical.

When discussing the orangutan, in particular, mention was made of its conflict with humans. The Sumatran orangutan is classed as critically endangered by the IUCN Red List with a decreasing population, and little hope for improvement at present. The major threats to the species are legal and illegal logging; a new road which, if approved, will further fragment the sparse populations; and competition with humans for resources.

One student said that the human populations have a right to live there, raise families and make money. Perhaps. “Human rights” are much talked about, and for the most part, our laws and customs are necessary and enshrined in our basic codes of behaviour for good reason.

However, human rights are a human construct: what marks us out as so special? It is difficult to view the world from a non-human-centred viewpoint, but sometimes this is worth trying. When looked at objectively and in a detached manner, it is not so simple.

Why should humanity have more “right” to resources than any other species? What about other species’ “right” to existence?

It has been suggested that other species, competing with us for resources, have a case to answer as to their right to survival. “Does it really matter if tigers survive?” asked a devil’s advocate? I would argue that, yes, it does matter. And not just because tigers are beautiful, majestic creatures; but because their disappearance may have far-reaching consequences for humanity. And, in any case, who are we to decide?

If we are competing in so many areas for limited resources, that does rather suggest that the problem lies within human populations. Our world is vastly over-populated – we are not just fighting other species for survival, we are fighting each other. Only by stabilising our own population growth can we begin to make any inroads into stabilising the world’s ecosystems.

Education is essential: both in the West and in the developing world. If we do not control our own populations, nature has a tendency to redress the balance. By studying animal populations, we can make predictions as to what may happen in our own populations: overcrowding breeds disease; overuse of antibiotics is producing many new strains of resistant bacteria; competition for resources starts wars.

Extinction, like death, is part of life and nature; there’s no denial there. Some species reach an evolutionary dead end. Some may argue that the mass extinctions we are facing are “natural”; I would disagree. Humanity is consuming resources so quickly and on such an unprecedented scale, that the world is shuddering in the face of too many changes. We are not just threatening other species – we are threatening ourselves. Perhaps this would not be such a bad thing for the planet; but people are (can be) amazing, wonderful creatures and we owe ourselves so much more.

The answer is not simple, and like almost everything else in life, the debate is not black and white. If conservation is to work – and it is a worthwhile task! – it will need to involve everyone: from governments, conservation groups and concerned individuals to the indigenous human populations themselves. Change has to come from within, and education is key here.

If we can’t find a way to protect and preserve the creatures we share this world with, what hope is there for humanity to improve, grow and evolve?

If it were up to me, resources would be poured into the conservation of those endangered species that have been directly threatened by anthropogenic activity alone. We have no idea what effect mass extinctions may have on the planet, on human health and society. Even if we cannot appeal to those who care nothing for wildlife and conservation, surely there is an argument to be made regarding the potential benefits of species we are losing?

And leaving aside all that, our world is incredibly rich and beautiful. Take a look around, learn a little more about the creatures that we are on the brink of losing. That in itself is a good enough reason for conservation. And it’s worth some measure of sacrifice.

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Welcome to the Dark Side…

…we have glucose…

Well, I promised you Photosynthesis Part II, and here it is. I have to say, I was most disappointed that it didn’t involve Voldemort, or a dark lord of any kind. Not even the Sith.

Anyway. The dark reactions are so called not because they take place in the dark, necessarily, but because they take place independently of the light – and the only place they happen is within the stroma of the chloroplast.

The light reactions gave us ATP and NADP.2H, which are used to drive the dark reactions. ATP provides energy for the process, while NADP.2H reduces (adds hydrogen to) carbon dioxide to a carbohydrate – a process also known as carbon fixing. So, if you like, ATP gives a plant enough energy to get its carbon fix.

The natural world is great at recycling – REALLY great at it. As NADP.2H is reducing carbon dioxide to a carbohydrate, it is, itself, being oxidised back to NADP – ready to be reused as an electron acceptor in the light reactions.

The whole process of the dark reactions is known as the Calvin cycle, after its discoverer – Melvin Calvin, whose parents had a terrible sense of humour when it came to baby names. I find it quite astonishing that back in 1945, scientists were able to delve this deeply into a plant cell and find out exactly what was going on.

A sugar phosphate with three carbon atoms as its backbone is the first product of the Calvin cycle, and it requires quite a lot of energy to make:

3CO2 + 9ATP + 6NADP.2H → 3C sugar phosphate + 9ADP + 8Pi + 6NADP

Some of the sugar phosphate is used as energy in the cytosol of the cell; the rest is converted into glucose phosphate and fructose phosphate, both of which are 6C sugars. These then combine to form sucrose, and lose their phosphate groups. Sucrose is transported around the plant for energy.

Photosynthesis is extremely well regulated and very efficient. Not to mention the fact that the light reactions are a truly renewable energy source – scientists are looking at their mechanisms, and wondering how to use the key components in artificial, light-driven fuel cells.

This is a brilliant idea, and I would suggest that any youth with an interest in photosynthesis, plant biology, and industry should get themselves on the rung of that ladder. It’s not just a career with a future; you may well be able to save our planet. And THAT is priceless.

This has been an exercise in ensuring that I understand photosynthesis; it’s rather complicated, you see. And it doesn’t make terribly interesting reading – so I promise that is the last long, boring explanation of a biological process there will be in this blog.

Plants are busy little things, aren’t they?

Today’s topic is the light-dependent reactions of photosynthesis. Now, you may think that it’s all fairly straightforward, thinking back to your GCSE biology classes (or O-Level for you oldies).

A bit of light for the leaves provides energy to turn water and carbon dioxide into sugar and oxygen. Simples, I hear you say. That is what I thought too. Just a short chapter, I imagined. How complicated can it be?

Well. Let me tell you that it’s very bloody complicated. I’ve drawn two diagrams, and I’m still not entirely sure I’ve understood it. And I’ve only done the light-dependent reactions! The dark reactions are yet to come. I’m expecting them to involve Voldemort in some way.

Here is a short account of the principle reactions involved in this stage of photosynthesis, which I wrote as part of an activity to help us to understand the processes. I would include my diagram, but I’m not drawing it on a crappy laptop. It’s not an Etch-a-sketch, you know. So I’ve pinched this one from my OU course book.

The light-dependent reactions of photosynthesis

The thylakoids are part of the chloroplast in plants. I apologise for the word “thylakoid”. All its consonants are in the wrong place, making it a bit of an assault course for the tongue. It reminds me of trying to learn German at school – I never was very good at German, partly because I had trouble getting my tongue around their words. I do, however, love the phrase: “Schnell, schnell, kartoppelkopf!”

They have an outer membrane, and a really convoluted internal membrane which is stacked into grana – and each little disc (or sac) in an individual granum is a thylakoid. The space inside the thylakoid membrane is called the thylakoid lumen, while the space outside the membrane is called the stroma. As illustrated above.

My summary is as follows. It’s supposed to simplify the description of what’s going on, and complement the diagram above. I’m not sure I’ve achieved that; any and all feedback is welcome!

When light strikes a chlorophyll molecule, a photochemical reaction takes place in which the hydrogen atoms of water molecules are split into their constituent protons (H+ ions) and electrons. (Oxygen is released as a by-product.) As shown above, the electrons move from the thylakoid lumen through the membrane to the stroma, by means of protein carriers within an electron transport chain (ETC). The protons are left behind, increasing the concentration of protons in the lumen. With me?

In the stroma, coenzyme NADP collects a couple of electrons and combines them with a couple of protons, reducing to NADP.2H (see above). This lowers the concentration of protons in the stroma. This will be important later.

One of the electron carrier proteins in the ETC is a little shuttle that collects protons from the stroma, bimbles across the membrane, and deposits them in the lumen, further increasing the concentration of protons in the lumen.

As a result of these processes, a transmembrane (yes, it’s a word!) protein gradient is formed across the thylakoid membrane – this works much like a hydroelectric plant (think of the reservoir at the top, and all that potential energy waiting to be turned into electricity). Now there’s an imbalance of proton concentration, enabling the protons to flow down the concentration gradient back into the stroma through channel proteins called ATP synthase (shown on the right of the diagram above).

The flow of electrons through these proteins enables the manufacture of ATP from ADP (adenosine diphosphate) and Pi and their transfer provides the energy required.

The products of these light reactions, ATP and NADP.2H, are used in the dark reactions of photosynthesis by the Dark Lord to reduce carbon dioxide to glucose.

I do apologise for the extreme biology – but this is the third time I’ve written the process in my own words, and I do believe it’s finally beginning to sink in. In a manner that ensures I understand and remember it.

Stay tuned for the Dark Reactions – I suspect they may be sexier.

Things that please me

A list. I like lists. Here is a list of things that please me:

  • The London Underground. I’m in love with it.
  • Animals on the Underground. How could you not be pleased with this?
  • Random photographs of people. Is this you? collects them from everywhere, including passport photo booths.
  • Cheese.
  • Small things. As in miniature versions of big things.
  • The way enzymes work.
  • Tea.
  • Putting on socks outside in the wind.
  • Hugs (but only from very specific people).
  • Having my hair washed.
  • Entering a just-cleaned bathroom.
  • Hanging out the laundry.
  • Stroking a cat.
  • Ticking things off a to-do list.
  • Gathering in the laundry.
  • Radio 4.
  • Uncaged monkeys.
  • Twitter.
  • David Attenborough documentaries.
  • Random acts of kindness.

Please note: this is not an exhaustive list.

The science of mouldy soup

TMA04

I must start this blog post with a bit of a “hurrah!” I have received my mark for TMA04 (Book 4: Chemistry). Drum roll… I got 92% – even with the “discussion” about one of the questions, and its ludicrous wording and requirements.

So, I’m very chuffed indeed. I understand chemistry. Or at least, I understand the basics, which will stand me in good stead for Book 5: Life – and, I hope, level two of my journey.

Mould

Activity 2.1 of Book 5 required me to investigate fungal particles in the air. In my kitchen, to be precise. So an experiment was undertaken. Bear with me… it’s aces.

The aim of this investigation was to estimate the density of fungal particles (spores) in the kitchen by exposing an appropriate growth medium (Sainsbury’s Basics tomato soup – I’m a cheapskate!) to a known volume of air, and then seeing how many fungi grow on it.

Equipment

Small can of Sainsbury’s Basics tomato soup

Rectangular plastic container

Paper and sticky tape to label container

Cling film

Ruler.

Experimental design

The container needs to be wide enough and deep enough to accommodate the soup, plus a reasonable volume of air. About half a litre should be plenty. A rectangular container will make it easier to measure and calculate the volume of air under the cling film.

By washing the container thoroughly, and drying it upside down, the likelihood of contamination will be reduced. To ensure that nothing else gets inside, the soup will be transferred to the container quickly, and then immediately covered with clingfilm. A second layer of clingfilm will be used to make the container airtight, thus preventing anything else entering the container.

The volume of air can be measured by multiplying together the length and width of the container, and then multiplying by the depth of air from the clingfilm to the surface of the soup.

It should be kept out of reach of children and animals, and where it is unlikely to be disturbed. Although I can’t imagine anyone – husband or cats – would look at that and think: “Ooh yum! I’m a bit peckish” and then dive right in…

How long should I leave it? Well, how long’s a piece of string? That will depend on how quickly mould forms on the soup. A week or so should be fine.

I will record the start and finish date and time, and record when fungus first begins to appear, and when it stops increasing.

What should I do with the container and its contents afterwards? Well, the OU recommends that I throw away the whole shebang – for health and safety reasons (excuse me while I stop laughing); however, I will dispose of the mouldy soup in the toilet, rinse the container into the toilet, then put it through the dishwasher for a thorough wash. I am not throwing away a perfectly good Tupperware container! That’s going to have my lunch in it tomorrow.

Practical procedure

The container was thoroughly washed and left upside down to dry. When it was dry, the can of soup was opened and quickly poured into the container. The soup was immediately

covered with two layers of clingfilm, and made airtight.

The experiment was labelled “Biohazard: not to be eaten”, and the date and time recorded

(May 31, 2011 at 7.30pm). The container

was placed out of the reach of the cats, and left where it was unlikely to be disturbed.

Biohazard: mouldy soup

The volume of air in the container was measured:

Depth from clingfilm to surface of soup: 3.0 cm

Width of container: 13.5 cm

Length of container: 18.5 cm

Volume    = 3.0 cm x 13.5 cm x 18.5 cm

= 749.25 cm3

= 7.5 x 10-4 m3 (2 significant figures) Note: the corners of the container were rounded, so this figure is approximate.

The first mould began to appear on June 4 and were tiny white spots (about 1 mm in diameter), mostly around the edges of the tub.

On June 5, the white spots had grown to a diameter of around 3 mm to 4 mm, with 1 mm green/blue patches in places. More areas of growth had appeared. Condensation also appeared on the clingfilm, which made observations a little awkward.

My mould was respiring! I was so proud. My very own baby mould; they grow up so fast.

By June 9, no more spots were appearing. And it’s probably a good thing, because it was getting a little crowded in there, and the patches were beginning to fight among themselves. I did NOT want to have to step in there and break anything up.

Results

The Mould Boyz

Seventeen separate areas of mould were counted. Most of the mould was clinging to the edges of the soup on the container, with a few patches in the centre. The patches in the centre resembled blisters lying just on or beneath the surface. They were milky in appearance, and slightly jelly-like, measuring 0.5 cm to 1.0 cm in diameter. Delicious.

The patches around the edge were either white, or white with green/blue areas. The white patches had stalks, while the green/blue mould was furry in texture. These patches measured around 1.5 cm to 2.5 cm across. I’ve seen this furry mould before; it normally inhabits the bit of sandwich you’ve just put into your mouth. You know this, because there’s half a patch of mould left when you look at your meal.

Analysis of results

Each area of growth probably represents one fungus, which arose from one fungal spore. My result was: 17 fungal spores per 7.5 x 10-4 m3 air.

To find the number of fungal spores per cubic metre of air:

= fungal spores per m3

= 2.3 x 104 fungal spores m-3 (2 significant figures)

I could work out the total number of fungal spores in the air in my whole kitchen; but frankly, I’d rather not know! I’m quite happily living in blissful ignorance, and perpetuating the dastardly rumour that I am, in fact, a great wife who cooks, cleans, maintains her rather great bottom AND makes interesting conversation that does not involve mould.

Critical thinking

The density of fungal spores I obtained is almost certainly an underestimate of the true density. This does not make me happy. I thought 22,666 spores per cubic metre was quite alarming enough.

Assumptions were made that the number of fungal spores in the air are evenly distributed throughout the room; this is unlikely to be the case, especially with movement of air. It may be that not all the spores trapped in the container grew into patches of mould. It was also assumed that all spores had grown into mould when I ended the experiment; this may not be the case.

Further investigations

We were supposed to think about what else we could investigate. But really, the only thing that came to mind was the mating habits of fungus. I suspect I’ve been staring at a screen for too long…

My next activity involves researching Leontopithecus rosalia. Stay tuned!

Why I love science

Most people who know me will know that I love science because I want to save the world. I’m horrified at what we’re doing to the planet and its beautiful animals and plants.

However, the other reason I love science is because of people like this extraordinary young lady: Krissi Fox.

I only discovered that she exists today. She has Acute Myeloid Leukemia, and blogs about it. Reading her blog may make you cry. But I’m almost positive that it will inspire you to be a slightly better person 🙂

Good luck Krissi. I think you’re amazing.

Farewell, sweet chemistry, for now

Well, I have reached the halfway point in my study of science with the Open University – farewell, Book 4. I have enjoyed you very much, and I do believe that we have surprised each other.

You surprised me by re-introducing me to The Mole, and making me love it. I surprised myself by not only enjoying chemistry, but understanding it too.

However, I must put in a complaint. Not about the chemistry, you understand; nor about the way in which it was taught (although really, some of the writers need to embrace the idea of “less is more”). No, my beef is with those who set the questions for the TMAs (tutor-marked assignments).

In this case, the person who required us to needlessly rearrange an equation, then arrange it back again, when we could find the answer quite easily using the original equation and the information in the graph – thereby confusing everyone on the course – should be punished by being locked in a room with Silvio Berlusconi and Celine Dion being played on a loop.

Failosaurus.

But apart from that little blip, the TMA is done and dusted, and is going through a checking process. I should have dispatched it by the end of the day today.

I feel I’ve achieved quite a lot from this module: I understand, do not fear, and in fact have grown to love Avogadro’s mole; I am able to write balanced chemical equations; I understand acids, bases and equilibrium; I can find the hydrogen ion concentration of a substance from its pH; and I am beginning to understand how drugs work (and therefore, how enzymes and hormones work). It’s really fascinating stuff.

Fuel, and evidence, is being added to my mini-crusade against quackery. Well, my own personal local crusade, partially inspired by Ben Goldacre (I had my doubts before I started studying science, and before I discovered his Bad Science writings).

I should clarify: the placebo effect is real, and documented, and I’m absolutely happy with that. What really grates my carrot is when people peddle something like homeopathy as “science”. Some homeopathic remedies are sold at a dilution of 200C. That means that one drop of the “remedy” has been diluted in 200 drops of water – 100 times over. It has been diluted more than the number of atoms in the entire universe. (Thanks to Bad Science for this nugget!)

And that is only one of the ways in which homeopathy is quackery.

But as I said – the placebo effect is fine. I have no problem with people parting with their hard-earned cash for nonsense, or for a placebo. What I DO have a problem with is quacks encouraging seriously ill people to stop their medication, and start taking sugar pills. That is dangerous, arrogant and pretty close to evil. I saw a forum discussion, via a tweet from Le Carnard Noir, in which homeopaths were talking about how to encourage HIV and AIDS patients to stop taking their retrovirals in favour of taking sugar pills.

And then one of them demanded that everyone else stop making a link between HIV and AIDS. That’s not just deluded, it’s dangerous. And vulnerable people, who are desperate, will listen to them.

I’ve also learned that when people say that, “Natural is better; chemicals are bad, m’kay” they have not really thought about what it is that they’re saying.

Salicylic acid - the active ingredient in willow bark

Take the example the OU gave us: aspirin was developed from willow bark, which has the active ingredient salicylic acid. In days of yore, willow bark was used to treat aches and pains, and was quite effective – except for the side effect of stomach irritation. Chemistry has enabled scientists to adapt the natural drug – salicylic acid – to acetylsalicylic acid, which does the same thing, but without the side-effects.Acetylsalicylic acid - the active ingredient in modern aspirin

Another example is Ventolin (or to give it its proper name, salbutamol). It mimics adrenaline, a chemical released by our bodies in times of stress. As it happens, adrenaline is very effective at opening the airways, thus relieving asthma – but the last thing an asthmatic wants is increased heart rate, changed blood flow, and the jitters. Salbutamol was developed from adrenaline, but tweaked slightly so it only affects the lungs, without affecting the other organs.

The natural remedy was a great start; but most people forget (or likely don’t think about it at all) that the plant evolved the chemicals for its own good; not for ours. Why would a natural remedy, “designed” to benefit the plant it came from, be ideal for use on humans with no tweaking?

Instead of bemoaning the work of modern chemistry, people should be celebrating it. It’s an incredibly creative area of science, and has saved and improved countless lives.