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Explosions and loose ends

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I have Explored Science.

I handed in my final, examinable assessment this week, and - bar the Grand Waiting For Results - my level one course with the Open University is complete. I have a very good feeling about the final assessment (the EMA); I enjoyed completing it, and didn't find it as frightening or difficult as I expected. I'm not sure if this is a good thing or not...

My feelings at the moment are mixed: I have adored this course with a passion normally reserved for cheese. It's been an eye-opening, mind-expanding, boggling and awe-inspiring journey, that has often afflicted me with a penchant for too many superlatives. But the Universe is a very large and splendid place, so the odd superlative isn't necessarily out of place.

However, I'm now both sad that the course has ended, and at a loose end. What now? I find myself wandering aimlessly around the house, tidying and generally finding Things To Do. I started by placing myself in the vicinity of a large glass of wine, but frankly there is only so much of that one can do before one becomes the local lush, so here is a run-down of my Saturday night.

Brace yourselves...

My esteemed and marvellous husband has invited his blokey colleagues to our house for a game of poker. Now, normally, I would take myself to my study and study furiously - but I have no studying to do! And worse - I have no broadband (this is having profound effects on my sense of civilisation; I'd be rubbish in an apocalypse that involves sending us back to the Stone Age) so this blog won't even reach cyberspace until who knows when. Which is now. Tuesday.

So what have I done with my Saturday night? Well may you ask. It has involved explosions, funk and groove. People: I have Done My Paperwork! Paperwork that has built up since March this year. I've filed, organised, stapled, punched holes and recycled like the crazy party animal I am. But before you write this off as a really dull way to spend Saturday night, bear in mind that I have been drinking Waggle Dance throughout, and that my hole punch exploded.

That's right; there are holes EVERYWHERE. My study is covered in holes. It looks like an example of chaos theory, which is appropriate to my course of study, but not to my innate and, some may say uptight, sense of order and tidiness. It's making my brain hurt. And I can't bring the vacuum cleaner in and sort it out until tomorrow, because Joe's colleagues will think I'm a mentaller.

Woe.

The Indian Summer will continue tomorrow, and I shall make a longbow and a knife. After clearing up the holes, of course.

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Quantum leap

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Edited by Vicky Fraser, Friday, 9 Sept 2011, 14:23

 

It appears that physics and I get on rather well. That is probably apparent from the recent fangirl posts; but now I have it on paper too.

A grand total of 93% for TMA07. I am delighted; it wasn't one of my better TMAs, and I really wasn't sure if I'd grasped it properly. I made a couple of silly mistakes - but I can't complain, and it's focused my eye for detail a little more closely on the detail!

Here's a musical interlude:

http://www.youtube.com/watch?v=DZGINaRUEkU

Book 8 has been pretty interesting so far; I'm searching for life elsewhere in the Universe (as ever) and the journey began by looking at the origins of life on Earth. How far back can we see? Are those tiny squiggles in the rock microfossils, or random arrangements of crystals, or just eye-worms in the heads of the scientists in question?

However long ago life sprang into life on Earth, we now have it on fairly good authority that the building blocks, at least, of life came from the stars, via the intervening space.

Comets brought water; meteorites brought organic compounds.

We haven't found life anywhere else in the Universe just yet. The chances are it's just too far away. But it's crazy to believe that we're the only life in the staggeringly vast space that we call reality. There are plenty of star systems like our Solar System, and no reason to suggest that there are no other Earth-like planets out there inhabiting that narrow band of space just the right distance from their star - and who knows what lives there?

I like to think that's where some of the creatures from mythology abide - Pegasus, the unicorns and the odd satyr, together with pixies, fairies and well-adjusted teenagers.

Will we ever visit a different world? Perhaps. Not by conventional means, but who knows what may be possible in the future.

One thing I do know for sure: this planet of ours is extraordinary and beautiful, and thinking about the chances of everything happening just at the right place and time is mindblowing. Not miraculous; just absolutely bloody fantastic.

Now, go and look at Symphony of Science.

 

Permalink 2 comments (latest comment by Vicky Fraser, Monday, 19 Sept 2011, 19:17)
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The end of days

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S104 is really picking up the pace now - I've just submitted iCMA 48, with 93%. So that's good then. And I'm zig-zagging through TMA07, which is due in on September 1.

Actually, it's going quite well. I still have trouble deciphering some of the question wording, and suspect that they are set by people for whom English is not their first language, but you can't have everything.

Sometimes, things just snap into place. You need to worry about them for a day or so, fret that actually, you're rather stupid and you'll never get this, and then it happens. A golden moment, a small firework in your mind, and there it is: enlightenment and understanding.

Question 2 (c)(i), I have the measure of you. I challenge you to a duel; pick your pistol. I'm confident, knowledgeable, and I shall have my satisfaction, sir.

I've very much enjoyed Book 7 - Quarks to Quasars. I've struggled a little with the specifics, such as energy levels, and the subtle effects electrons have on one another, not to mention the strength of the various interactions. But the concepts, the wider questions that border on the philosophical as well as the scientific - those, I love.

The feeling of stretching your mind so wide open that you feel it's entirely possible there may be a permanent split is a heady rush. Have you ever stood on the edge of a cliff, or a very tall building, and had that momentary - just a split second - urge to throw yourself into the void? It's a little like that.

The Universe started as a very dense, very hot mass of energy, then exploded and expanded. But how? Where did the energy come from? Was it always there, or did it just pop into existence? Lawrence Krauss maintains that yes, it came from nothing. I'm afraid I can't accept that - which is why I shall keep reading, and watching, and learning.

And what about the "edges" of the Universe? What is it expanding into? Well, nothing that we can comprehend. The Universe has no edges, so to speak. It is everything. Or, it is everything in our comprehension. But that is not to say that there isn't some"thing" out there beyond that, far beyond our comprehension, made of stuff that we could never know...

The more I learn about our Universe, the more fascinating I find it. I worried that I would lose the meaning of life if I was truly convinced of how insignificant we are - but, if anything, I have experienced the opposite.

Perhaps everyone has (or wants, or needs) to believe in something. I'm not sure. I don't believe in a god, I know that now. This worried me for a time, as I see some of those I care for deeply, and their faith gives them strength and purpose. What would I have? I think my drive comes from a deep-seated desire to understand our Universe, to find out as much about it as I can. I believe it is within our grasp as a species, if we can manage not to destroy ourselves first. And what we find out may turn out to be completely unexpected.

And, I have faith in people. They are extraordinary.

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Exploring Science

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As this blog is following and documenting my adventures in science, it seems that I should say a few words about S104 Exploring Science for any prospective students of the Open University.

I'll start by stating, in no uncertain terms, that this is a Very Difficult Course, particularly if there is no (recent) background in studying science or maths. This is not a light, adult-learning-style, interest-only course: it's full on, in depth and requires an awful lot of hard work.

If any prospective students are not truly interested in science and really committed to learning, it will be extraordinarily difficult. I work full time, and I try to have a social life too - I have struggled to find the hours required for this course.

However, and I can't emphasise this enough, S104 Exploring Science is absolutely bloody brilliant. It is Professor-Brian-Cox-jazz-hands-brilliant. Finding the time to study has not been, in any way, a chore.

Some aspects of the syllabus have been easier than others; some have interested me more than others. But overall, it's fantastic.

Here, I need to pay tribute to my wonderful husband - I could not have done this without him. He has been supportive, interested, helpful (especially with the maths and physics) and he has become a very good cook. Joe's patience is seemingly never ending, and I know he's really proud of me. I am proud of him. And I am so grateful.

Anyway. Enough mush. Here are the facts, figures and ravings of an S104 Survivor.

For those thinking of starting S104, I would recommend that you do some reading first - partly to see if you really are that interested in science, and partly because it will give you a good base to build upon. I found Ben Goldacre's Bad Science to be a great introduction to scientific method, and it's a good read to boot. His blog is fab.

We Need to Talk About Kelvin by Marcus Chown is also a good read. One of the more wonderful moments of this course was when I realised, in a bolt of inspiration, that I actually understood what I had been reading about a few months earlier.

And as preparation for when you arrive, breathless and exhausted, at the bottom of the mountain that is Quantum Physics, give Jim Al-Khalili's Quantum: A Guide for the Perplexed a whirl.

In fact, just read everything you can get your hands on, in the daily media, online and in journals such as New Scientist.

Before beginning, brush up your maths. Maths used to terrify me. It's well worth doing the Open University's freebie maths book to start.

Exploring Science is a nine-month course, and the course team recommends that a minimum of 16 hours per week is put aside for study. I have found this to be fairly accurate, albeit the study time is probably an average. Most people will find some topics require far less work, while others require much more (biology and quantum physics, please stand up!) .

There are eight books covering different topics, and although the order may seem slightly odd when you first see it - it does all fall into place:

  • Book 1 - Global Warming. This is a fairly gentle introduction to S104, and jumps feet-first into a subject that is bang up-to-date - climate change and all that goes with it.
  • Book 2 - Earth and Space. Geology and geological processes are introduced in part one, while in part two we leave Earth and venture out into the Solar System. Again, this is not too taxing, and is a decent way to ease you in.
  • Book 3 - Energy and Light. Physics-lite - I began this book reminiscing about GCSE physics, and remembering a surprising amount. By the end of the book I realised that this was Grown Up Stuff, leading my thoughts in directions they would never previously have contemplated. The maths began to pick up pace; and rather than becoming baffled and afraid, I developed a deep and abiding love for a beautiful and elegant discipline.
  • Book 4 - The Right Chemistry. Again, it begins with a recap of GCSE chemistry, then steamrollered into the kind of stuff that makes you wonder if, by the end of the course, you'll be able to run your own meth lab. Fascinating. And if, like me, you were once afraid of the mole, this book will cure your fear.
  • Book 5 - Life. Biology. It's the thickest book of the lot, and it's stroppy with it. Life lulls you into a false sense of security, starting with the difference between autotrophs and heterotrophs, looking at prokaryotes and eukaryotes, before steaming into the minute detail of the reactions that make up photosynthesis. Think you know how plants make their food? Think again!
  • Book 6 - Exploring Earth's History. An interest in fossils and geology will mean you sail through this book. It's absolutely fascinating, and is a grand illustration of how absolutely everything in our Universe is connected. Our planet is a staggeringly beautiful and complicated place, and I am humble before it.
  • Book 7 - Quarks to Quasars. Mind-bending stuff. But give it time, read everything VERY carefully, more than once, and it WILL make sense. I promise. I found that writing notes in my own words was really helpful.
  • Book 8 - Life in the Universe. I'm not there yet. But the book promises to pull together all the aspects of S104, enabling us to build a complete picture of how the separate disciplines tie together. All branches of science are connected, and feed into each other. It will be good preparation for the End of Module Assessment.

Everybody's techniques for studying are different, but this is how I approached Exploring Science. As I read through each chapter, I highlighted relevant concepts, ideas and facts, making notes in my own words. I also, as you have probably gathered, began this blog. It is, in part, a method of finding out if I've fully understood what I'm learning: if others understand my tales and explanations, it's a good bet that I have.

Talk to your loved ones: bore them silly! I am lucky to have a husband who is almost as fascinated by this stuff as I am, and many of my friends are crazy about science. (I thank you all so much for listening, reading and generally being interested. I love you guys!)

Use the tools the Open University gives you: do all the activities, because they really do consolidate your learning, as well as being good fun in many cases. The questions dotted throughout the text are brilliant, testing your knowledge and understanding before you come to do the assessments.

And speaking of assessments: at the end of each book, you are required to complete an iCMA (interactive computer-marked assignment) and a TMA (tutor-marked assignment). These contribute to your overall mark, as well as helping to pull together everything you've learned.

A good tactic for the iCMAs is to write them out in rough before you enter the answers. My first one was pretty shameful, purely because I hadn't read the instructions properly! In my excitement at starting the course, I achieved only 80%...

For the TMAs - read the questions really, really carefully! Sometimes the OU examiners do not use language in the way you may expect... I found that leaving the TMAs right until the end of the book meant that I was a little stressed about getting them in on time. The questions helpfully tell you which chapters you should have finished before attempting to answer - I would advise that the TMA is completed as you go along.

Use your tutors, that's what they're there for. They are a great source of support, if you're lucky enough to get a really good, dedicated person. The tutorials are also a good source of support, as well as helping you meet other students.

Use other students too: the tutor forums can be helpful, if you get a good group - or join the S104 group on Facebook. I've made some lasting online friends through that, and it's made me laugh until I cry on more than one occasion. You are not struggling alone.

And finally: enjoy it! It's been a fantastic experience, and I'm genuinely sad at the thought of the course ending (although I cry at the news, so don't let that be a measure of normality...). Good luck, and remember:

"What we have learned is like a handful of earth. What we have yet to learn is like the whole world." Avvaiyar, Indian poet-saint.

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Interlude

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I've been on holiday to the beautiful, wild, staggering Scottish Highlands. Achmelvich, Skye, Poolewe and Applecross, to be precise. So there has been little blogging, and a small holiday from studying.

Tomorrow, I shall be blogging about many things quantum. But for now, I shall leave you with this quote, spoken about physics and chemistry, but true of all things:

"Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less." Marie Curie, Polish-French chemist and physicist, and winner of two Nobel prizes.

Peace out.

Permalink 1 comment (latest comment by Mark Cameron, Tuesday, 16 Aug 2011, 21:55)
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Everything must flow...

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Edited by Vicky Fraser, Wednesday, 20 July 2011, 21:19

Everything is connected. Absolutely everything. From the more obvious water cycle, to the less obvious carbon cycle, to the frankly astounding and mind-boggling fact that we are all made of stardust.

Simple, observable, everyday phenomena tell us an enormous amount about how the Earth works. For example, I found out during my study of Book 6: Exploring Earth's History, where that yellowy-orange dust comes from. You know the stuff, it ends up on your car sometimes after it's rained. That is dust from the Sahara desert, and it only appears after a big sandstorm.

sahara-desert-6.jpg
Sahara dust makes its way to our cars

The fine, red dust is carried up into the lower atmosphere by the wind, and - if it's fine enough, and the wind is blowing in the right direction - it is transported to our little island and deposited on our cars (much to the annoyance of my dad - it's an abrasive dust, you see, and if you scrub at it the paintwork is damaged).

In the past, dust from all over the Northern Hemisphere was swept up towards Greenland and deposited on the ice cap in the fresh fall of snow. Millenia later, some of our more extraordinary adventure-scientists (I think that's a reasonable title for them) journeyed to the Arctic and took samples from the ice.

These ice cores tell us, amongst other things, how our climate has changed over the past 140,000 years. They show us the peaks and troughs of temperature, give clues as to how arid or humid the climate was, and tell us about the chemical composition of the atmosphere.

All this comes from the presence of dust in ice, and the proportion of heavy or light isotopes of oxygen (that's 18O or 16O) in the snow that fell on the ice-cap.

hudson_bay_oldest_rocks.jpg
The oldest-known rocks on the planet

Another use for isotopes is in radiometric dating of rocks. The oldest rocks we know about are around 4,280 million years old and occur in Hudson Bay, Canada*. That's not long after the Earth and the other planets of our solar system formed (about 4,560 million years ago). They are pretty rare; rocks tend to get recycled during tectonic activity.

Rocks are, against all probability and expectation, extraordinarily interesting. Not only do they provide humanity with gems such as diamonds and emeralds; they provide us with fossils. Look at the rocks next time you see a cutting by the side of a road. Really look at them. That layering, if you're in an area of sedimentary rocks, is giving you a snapshot of the past. You're looking into prehistory. There may even be fossils in there.

Connected to this geological time-line are deep-ocean cores - the sediments laid down by erosion and the dead organic matter in the seas. They provide another means of establishing a relative time-line - and it's all calibrated by the radiometric dating of rocks.

The study of rocks gave us the cause of the last mass extinction, that of dinosaurs (and a huge number of other families) in the K-T event about 65 million years ago at the end of the Cretaceous Period and the beginning of the Cenozoic Era. It's called the K-T event because scientists are awkward so-and-so's: K comes from the Latin for chalk - "kreta" (for Cretaceous) and T comes from Tertiary (an obsolete - but still used to confuse us students - name for the Cenozoic Era. And here is where I feel old: I'm sure I remember reading in books when I were a wee lass the name Tertiary. Cenozoic is a new one on me).

So what did cause the extinction of the dinosaurs? It probably wasn't one single event (and it's pretty much agreed that the other mass extinctions were not caused by a single catastrophic event, but by a combination of changing conditions). There were two events that happened at around the same time, on opposite sides of the world: a 10km meteor smashed into Mexico (you can see the crater on topographical maps) and in India there was, over the course of a couple of million years, an episode of flood-basalt volcanism.

The consequences of a meteor impact are fairly obvious: shockwaves, quakes, but mainly the dust, debris and gases entering the atmosphere. This would only last for a few months; but a few months of starvation is all that is needed to knock a species to its knees. Or its tentacles, if it has no knees. In short, the knock-on effect would be enormous (everything is connected, you see).

Likewise, the volcanism across the world would have a similar effect in terms of gas and dust - but spread over a longer period. CO2 and SO2 levels would rise, increasing the global mean surface temperature (they're greenhouse gases) - but at the same time, the dust in the atmosphere would increase the planet's albedo (the amount of sunlight reflected back into space). So overall, the planet would cool, and the rain would be acid.

This had the devastating, but on the surface insignificant, effect of collapsing a population of plankton because it couldn't photosynthesise. Of course, everything above it in the food chain suffered as well...

Although these events were natural, they should be a cautionary tale to us humans. Every action has consequences. A change to the atmospheric composition can have far-reaching effects; alter the pH of the sea, and the consequences could be devastating. We don't fully understand how it all works yet; but we know that changing one tiny variable will alter a dozen more in ways that we can't necessarily predict.

Everything is connected, and it can tell us an enormous amount about ourselves; our past, present and future; where we came from, and where we might go.

To those who say that science takes the mystery out of life: you are so wrong - if anything, it deepens it and whets the appetite for knowledge and understanding. And you are missing out on the adventure of a lifetime.

*The image of the Hudson Bay rocks was borrowed from here:http://www.daviddarling.info/archive/2008/archiveSep08_1.html. I thank the photographer, but will certainly remove it if requested!

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Biological joviality

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Edited by Vicky Fraser, Wednesday, 13 July 2011, 14:00

I've the afternoon off work to complete the Tutor Marked Assessment for Book 5: Life. And I haven't blogged in a while. I am also Sick with an unknown malaise of the throat. So, I give you: Biology Jokes!*

Biology is the only science in which multiplication is the same thing as division!


Did you hear about the famous microbiologist who traveled in thirty different countries and learned to speak six languages? He was a man of many cultures.


Confucius once said, "When you breathe, you inspire, and when you do not breathe, you expire."


The bad news is that the American Society for the Prevention of Cruelty to Amoebas is shrinking. The good news is that none of the amoebas has lost any of their members.


At NIH (National Institute of Health), there is a sign on the door of a microbiology lab that reads "STAPH ONLY!"


Q: What is the fastest way to determine the sex of a chromosome? A: Pull down its genes.


The teacher asks, "Jessica, what part of the human body increases ten times when excited?" Jessica blushes and says, "That's disgusting, I won't even answer that question."

The teacher calls on Johnny: "What part of the human body increases ten times when excited?" "That's easy," says Johnny. "It's the pupil of the eye."

"Very good, Johnny," responds the teacher. "That's correct."

She then turns to Jessica and says, "First, you didn't do your homework. Second, you have a dirty mind. And third, you're in for a BIG disappointment."


A man goes into a bar and asks: "Can I have a pint of energy please?" The barman pulls the pint and says: "That'll be 80p please!"


Enzymes are things invented by biologists that explain things which otherwise require harder thinking.


Did you hear about the biologist who had twins? She baptized one and kept the other as a control.


One day the zoo-keeper noticed that the orang-utang was reading two books - the Bible and Darwin's Origin of Species. In surprise he asked the ape, "Why are you reading both those books?"

"Well," said the orang-utang, "I just wanted to know if I was my brother's keeper or my keeper's brother."


It has recently been discovered that research causes cancer in rats.


I do apologise. I'll get me coat! *Shamelessly stolen from the Internet.

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Whose right to life?

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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...

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…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.

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Plants are busy little things, aren't they?

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Edited by Vicky Fraser, Thursday, 16 June 2011, 10:54

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.

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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.

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Farewell, sweet chemistry, for now

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Edited by Vicky Fraser, Thursday, 2 June 2011, 08:30

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.

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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.

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The nature of acids, and a long string of hydrocarbons

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I am charging through Book 4: The Right Chemistry, and after a shaky start, I'm enjoying it very much.

Last week I undertook an experiment to measure the acidity or otherwise of common household substances. It was just like being back at school, and I got to Make A Mess in the kitchen. Win!

I tested washing up liquid, shampoo, stain remover, laundry powder, tonic water, cranberry juice, bleach, tap water - and resisted the urge to plunder the house for anything that could have a Universal Indicator paper stuck into it. Including the cats.

I was very surprised at how acidic tonic water is - it has a pH of 3. So, what is pH?

pH stands for "potential hydrogen". I didn't know that, and don't remember being told at school (although it is entirely possible that I was setting fire to a bunsen burner at the time). This makes sense, however, as I now also know that the pH is a convenient way of describing what a substance's hydrogen ion concentration is.

So, tonic water has a pH of 3, which means that its hydrogen ion concentration is about 1.0 x 10¯³ mol dm¯³. Handy. Saves using lots of very small numbers and scientific notation.

Acids yield hydrogen ions when they are dissolved in water - so the higher the concentration of hydrogen ions, the more acidic the substance. Bases yield hydroxide ions: so the more hydroxide ions contained in a solution, the more basic that solution is.

The strength of an acid is determined by how far it dissociates in solution - hydrochloric acid, for example, is a strong acid because it dissociates almost completely. Almost all the HCl molecues dissociate to give positive hydrogen and negative chloride ions; whereas vinegar (acetic acid - or ethanoic acid, to give it its proper name) is a very weak acid as it only partially dissociates in solution.

The book then took us through the method of calculating a substance's pH from its hydrogen ion concentration - or vice versa. And very simple it is too. I can imagine it will come in very useful to you all on a daily basis - if for no other reason than to impress people in the pub.

"See that pint? It has a pH of 4.5, which means it has a hydrogen ion concentration of 0.0000316 mol dm¯³."

Anyway. I'm pleased with my progress, and have moved onto hydrocarbons. Which are pretty cool.

I am a long string of hydrocarbons. As are you. And so is almost everything, in fact. Including crude oil.

Hydrocarbons are subdivided into alkanes and aromatics. Alkanes are further subdivided into linear-chain alkanes, branched-chain alkanes, and cycloalkanes. This are all pretty good descriptions of their molecular structures.

Carbon has a valency of four, meaning that it can hang onto four other atoms. Hydrogen has a valency of one, so it can only hang onto one other atom. Linear-chain alkanes are long strings of carbon atoms attached to a maximum of two other carbon atoms, and two or three hydrogen atoms. These alkanes can also be folded over; they needn't be long, straight strings.

Branched-chain alkanes are similar to linear-chain alkanes, but instead of having two hydrogens, a carbon atom will be attached to a third carbon, forming a "branch". Hence the name.

And cycloalkanes are rings of carbon atoms, with hydrogen atoms attached. These, too, can have branches.

Aromatics are also rings of carbon atoms, but some of them have double bonds, and some of them single bonds.

All this is useful for grading petrol, believe it or not. When you're filling up your vehicle, the unleaded nozzles have "95" or "97" printed on them. These are the octane numbers; and the higher the octane number, the better the performance of the petrol. Y'see, linear-chain alkanes don't make very good motor fuel - they burn unevenly, and cause the engine to "knock" (small explosions interrupting the burn). Branched-chain and cycloalkanes are much better; and if you can add an aromatic to the mix, then it's better still.

I'm not sure why yet; I'll get back to you when I've found out.

I'm particularly enjoying hydrocarbons as I get to draw molecular structures. This pleases me: they are very regular, and appeal to my sense of neatness. This is ethane:

ethane.jpg

And this is an aromatic - napthalene - note the double bonds, and pleasant circular structure:

napthalene.jpgI've downloaded a chemistry drawing package to use for my Tutor Marked Assignment. I'll see how I get on with that...

I'm looking forward to Book 5: Life - and am hoping it will give me more of an idea of my future studying direction. I love everything so far - but I think a focused four-directional future will be time-consuming to say the least...

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An experiment to investigate light in the style of a pirate

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Edited by Vicky Fraser, Tuesday, 12 Apr 2011, 21:32

I have had a lovely weekend in the sunshine, much of which has been spent outside in our garden, under the beautiful cherry tree, on our new garden furniture. I've been pottering around, weeding the vegetables, planting more seeds, and watching the cats chase motes of dust.

In between, I've been studying hard - book 3, Energy and Light. I'm almost there; I've completed most of TMA03; all I needed to do was Activity 11.1 - Investigating Light.

Joe and I liberated a cardboard document box from his offices, and I planned my experiment. It is set out below, just as it is in my folder (with perhaps just one or two embellishments, and an extra instructive illustration). Some of the details have been changed and the first-person voice has been used because the write up was part of the assessment, and so cannot be made public for fear someone may plagiarise me. So some of this may or may not be true!

Investigating light: determining the wavelengths of spectral lines from an energy-saving light bulb.

Equipment

  • Diffraction grating (300 lines per mm)
  • Tungsten filament light bulb (40 W)
  • Energy-saving light bulb (11 W)
  • Lovely stripy table lamp (for the tungsten bulb)
  • Tall standard lamp (for the energy-saving bulb)
  • Large cardboard document box
  • Pieces of Amazon book cardboard
  • Gaffer tape
  • Sharp knife
  • Paper protractor
  • Blu-Tack
  • Black cotton thread
  • Red drawing pin
  • Dressmaker's pin
  • Eye-patch
  • Table
  • Dressing gown

Aim

To determine the wavelengths of blue, green and red spectral lines from an energy-saving light bulb.

Method

Having liberated the box from Joe's work in a ninja-style midnight operation, I cut a thin slit in it using the sharp knife. Joe took this off me, and did it properly with a minimum of blood spilled. I tidied the edges using gaffer tape. Gaffer tape can do anything: FACT. The table lamp containing the tungsten bulb was placed within, and Amazon cardboard was cobbled around the edges, in an attempt to prevent too much light from escaping and having a party where my spectral lines were supposed to be.

I had a gander through the diffraction grating, and this is what I saw - a continuous spectrum:

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This is an actual photograph I took *proud*
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Professional pirate dark-room. Eye patch provided.

Next, I needed to take a look at the spectrum produced by the energy-saving bulb. So I undid my gaffer-taped masterpiece, and fumbled the floor lamp with the energy-saving bulb under there. I couldn't quite manage to see the spectrum this time, so I created a dark-room, thus:

This created the ideal conditions to observe and photograph my diffraction spectrum - which was not continuous, and was in fact a line spectrum. Again, I photographed it:

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Line spectra from an energy-saving bulb

All this was very pretty, but had to be interrupted by a trip to Charlie's to make me a longbow. You see, my marvellous husband (he of the fabulous presents) bought me A Big Piece of Wood for my birthday. Not just any piece of wood, mind; a piece of yew, laminated with maple and lemon wood. He, Charlie and I began the shaping of a (very) long bow. It's going to be grand!

Back to science.

Later, when darkness had fallen, I continued my experiment and set up my equipment. Leaving the box with the energy-saving bulb where it was, I stuck it down to prevent any disastrous movement, and placed a paper protractor about 50cm away. A drawing pin pierced the protractor, to provide an anchor point for the thread. The diffraction grating was placed upon the protractor at the axis. Thread was tied to the drawing pin and the dressmaker's pin, and all was ready. See:

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Experimental set up.

This is where the eye-patch comes in. To measure the angle of diffraction for each spectral line, you have to line up the spectral line itself with the line on the grating and the thread upon the protractor. This is to be done with one eye, to prevent parallax error. I found myself unable to do this, and so had to use an eye patch.

Of course, it naturally followed that I had to conduct the rest of the experiment in the manner of a pirate. Grog was acquired, and duly consumed. Tables were swabbed, angles were swashed, and the thread was buckled. Much like my knees.

The experiment was a success! The wavelength of the blue, green and red spectral lines from the energy-saving light bulb were calculated as: 450 nm,  550 nm and 600 nm respectively. This isn't far off the actual wavelengths of light emitted by an energy-saving light bulb. Go and google it if you don't believe me.

This has been Science, by Vicky. I've enjoyed it; all that remains to be seen is how well my tutor likes the write-up... I do think that the eye patch was relevant. And the dressing gown.

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Beautiful mathematics

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Edited by Vicky Fraser, Thursday, 24 Mar 2011, 18:53

I am a well-known hater of mathematics, largely because of my (perceived) lack of ability. So it came as some surprise to me that I am very much enjoying Book 3: Energy and Light of S104: Exploring Science.

Algebra is the topic in hand, and we’ve gone right back to basics.

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I would quite like this t-shirt.

I remember, as a small child, that in junior school I and several other bright (read geeky) kids were part of an algebra group. The headmaster had a little maths geek set going on, and I was IN. It wasn’t the best school in the world, and the town was... well... provincial. An ex-mining town, very working class, with fewer aspirations flying around than I or my parents would like.

However, I believe that this school (Stockingford Middle School) and this teacher (sadly I cannot remember his name) did me a great service: they stoked my interest in science, and planted in me a very deeply buried love of maths. Or at least, the beauty of maths.

I wasn’t to know, yet, that algebra could enable you to produce very cool images, such as the one on the right...

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Groovy.

It stayed buried for a long, long time. Throughout senior school, I loathed maths - partly, I suspect, due to an uninspiring teacher who was convinced I’d fail my GCSE (I got a B) - and partly because I just convinced myself it was too difficult, and I couldn’t do it.

Enter the Open University, S104, Book 3. They really do start at the basics, and I remember more than I thought, so I’m powering through the work; spinning through the vast, echoing spaces in my mind with equations creating beautiful symmetry all around.

Or something similar...

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In the beginning...

There is something very calming and aesthetically pleasing about rearranging equations. I like balance, and order, and that is what an equation is. Balance. Yes, it’s simple; but I’m enjoying it. And what’s more, I’m looking forward to the more complex stuff...

Maths is everywhere. Nature, science, art, beauty... Poetry, according to Betrand Russell, who said this:

“Mathematics, rightly viewed, possesses not only truth, but supreme beauty - a beauty cold and austere, like that of sculpture, without appeal to any part of our weaker nature, without the gorgeous trappings of painting or music, yet sublimely pure, and capable of a stern perfection such as only the greatest art can show. The true spirit of delight, the exaltation, the sense of being more than Man, which is the touchstone of the highest excellence, is to be found in mathematics as surely as poetry.”

He’s right, too. I’m just beginning to understand why maths is so important, how it is a part of everything in the Universe, and appreciate its purity and its sublime beauty.

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Dumbing down?

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Edited by Vicky Fraser, Monday, 14 Mar 2011, 12:58

Last night, the second episode of Professor Brian Cox’s Wonders of the Universe was shown on BBC2. I am loving this series so far; and I really enjoyed its predecessor, Wonders of the Solar System.

Last night’s episode tied in perfectly with what I’m studying at the moment as part of S104 - Exploring Science. I’m looking at the composition of stars, how they work, how they are born, live and die. The show did a great job of illustrating and supplementing what I’ve been learning.

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I am the type of person who finds it very difficult to grasp difficult ideas quickly. I can’t just read about a concept and understand it; I’m quite envious of those who can do that. So I look for all sorts of different ways to learn about a topic - and if there are pictures, diagrams and analogies, so much the better.

This series is not aimed at those who already know all there is to know about the universe; it’s aimed at people who don’t know much at all, or at those of us who devour everything they can about the subject, whether it’s simple or not.

There is plenty of other information out there on science, but much of it is not easily accessible to the masses - and some of it is a bit dated. Science is constantly evolving. We are always learning new things, constantly revising what we know and what we think we know.

Some people will say Wonders of the Universe is science-lite; dumbing down for the masses. I disagree. Simplified doesn’t necessarily mean wrong, and it certainly isn’t a bad thing. My OU course simplifies things all the time. So do scientists. I think Prof Cox is very good indeed at taking a really complicated idea and presenting it in such a way that those who have never studied science or astronomy can grasp it. His enthusiasm is a joy to see.

I can quite understand how some people would find him irritating; he’s a bit of an acquired taste, and he can be a little odd. But I like him, and I like the way he presents his subject with simplicity and enthusiasm - although, as a friend has pointed out, the series is a little like the great Michael Palin’s travel diaries in places... But who wouldn’t take that job if it were offered to them?

Accusations of being terribly trendy have been levelled at him and his fans - but is that such a bad thing? If jumping on a bandwagon gets people interested in science, surely that can only be a good thing. It’s a sad fact that many people are more interested in celebrity nonsense than in things that actually matter - so if Prof Cox is using his popularity and “trendiness” to get people to watch and learn: good for him!

Most people will get no further than this TV series - but a few will fall in love with science and knowledge because of it, and will go further, read more, perhaps even take up some science study. That’s priceless.

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In the Beginning...

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...there was a Big Bang. Or something similar. And Stuff came into being. That Stuff mingled, and meandered, and heated and cooled; and amongst a lot of other things, Planet Earth emerged.

Then it was populated with plants and animals. Some of those animals were Us.

I would quite like to know how all this happened, and how it all works, and how we can stop ourselves from destroying it all.

This beautiful planet is home, and I love almost everything on it. (The exceptions being sprouts and wasps; but I do understand that they may be useful in some ways.) I think we should look after our home, and understand how it works. And marvel at it, appreciate it and cherish it.

I'm not a total yoghurt weaver (although that last paragraph somewhat contradicts this statement) but I want to Save The Planet. Through the medium of marine biology. So, having no scientific background, and little spare cash, I have embarked upon a voyage of discovery with the Open University.

S104: Exploring Science is where I begin. Which is appropriate, as that is what I want to do. Explore.

So armed with enthusiasm, wide-eyed wonder, and an array of equipment (esoteric and mundane) I wade into the myriad facts, figures and tales of the divine in my quest for knowledge.

This blog will record my learnings, my successes, my (hopefully very few) failures, and my musings on this voyage.

Good luck to all those embarking on a similar journey; and to those who are just curious - I hope this may inspire you to wander into uncharted territory also.

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