Motility Symbiosis - A Clue to Cellular Evolution?

Swimming inside the gut of the drywood termite Cryptotermes cavifrons is a remarkable microorganism called Caduceia versatilis¹. C. cavifrons and C. versatilis share a symbiotic relationship – that is, a partnership between two species from which both parties benefit in some way. The tiny protists inside the intestines of the termite help it to digest wood², allowing it to absorb the products it needs, whilst it provides a food source and habitat for the protists³.

What is so special about C. versatilis? The answer lies in the way in which it moves through the gut of the drywood termite. Looking through a microscope, it would appear at first that the microbe propels itself forward by the wavelike motion of tail-like structures called flagella, as is the case in many species of bacteria⁴.

In fact, the surface of the protist cell is lined with thousands of even tinier rod-shaped bacteria called spirochetes. These bacteria possess their own flagella, which rotate in perfect synchrony to create a wave of movement that propels C. versatilis forward. In other words, the protist is involved in another symbiotic relationship – the rod-like bacteria on its surface actually allow it to move through the gut of C. Cavifrons⁴. This type of symbiosis, ­­in which bacteria confer the ability to move onto their partners, is called motility symbiosis⁵.

Motility symbiosis is a rarely documented phenomenon; another of the few known examples of it is in a protist called Mixotricha paradoxa¹. Yet, believe it or not, it could hold a clue to a question upon which biologists today are still not agreed. Let’s take a look at the cells of eukaryotes (animals, plants, fungi and protists).

Many eukaryotic cells have their own flagellum-like tails, sometimes referred to as undulipodia as they differ somewhat in structure from the flagella found on bacteria⁶. Undulipodia also include cilia, small hair-like organelles which are found, for instance, in the windpipe of humans where they beat back and forth to keep our airways clear of dirt and mucus⁷. The whipping motion is driven by the action of special proteins inside undulipodia called motor proteins⁸.

The question, then, is: how did undulipodia arise in the first place? Most biologists believe that they evolved gradually from the flagella of prokaryotic cells, their structures changing as they became more specialised and adapted to the needs of eukaryotes. For example, undulipodia are considerably thicker than bacterial flagella and move in a whipping fashion rather than a rotating one⁶, which may be evolutionary adaptations to the bulkier size of eukaryotic cells: undulipodia which propel cells forward, such as the ones found on sperm cells, must be able to create a larger driving force in order to move a heavier cell.

This idea, known as autogeny⁶, is just one hypothesis, and in 1970 a biologist called Lynn Margulis proposed a more radical one: that somehow, undulipodia could have evolved from the symbiotic relationship of an immotile cell with a type of flagellum-possessing bacterium called a spirochete. This is where we come back to the idea of motility symbiosis: from the examples we have discussed above, we already know that it is possible for a symbiotic relationship to exist in which a bacterium confers motility onto another organism by effectively lodging on the membrane and rotating its own flagella to drive both cells forward. Margulis proposes that, at some point in evolutionary history, a spirochete and a eukaryote somehow fused together to form a single cell with the first undulipodium. This eukaryote, now having a competitive advantage over its peers in that in can move independently, would have been favoured by natural selection and hence undulipodia became widespread in eukaryotes.

This idea of endosymbiosis is vastly different to autogeny, which proposes gradual evolutionary changes, but Margulis argues her case strongly, claiming that undulipodia are more closely related in structure to spirochetes than to ordinary flagella⁶. Most biologists are sceptical about the origin of undulipodia by endosymbiosis due to a lack of supporting evidence – for example, if undulipodia were once free-living bacteria, why do they not contain their own DNA? – but Margulis’ hypothesis has not been rejected completely. Her appeal to existing cases of motility symbiosis in today’s biosphere, such as that in C. Versatilis, as evidence for endosymbiosis is perhaps a strong one – but, on the other hand, it could be a mere coincidence. The origin of undulipodia could be one of those great mysterious questions in science which will never be answered for definite.

References

1 Biology of Termites: a Modern Synthesis – D. E. Bignell, Y. Roisin, N. Lo (2011) – 15.7.3: Motility Symbiosis

2 Featured Creatures: Cryptotermes cavifron – A. S. Brammer, R. H. Scheffrahn, University of Florida (2002)
4 The Motility Symbiont of the Termite Gut Flagellate Caduceia versatilis Is a Member of the “Synergistes” Group – Y. Hongoh, T. Sato, M. F. Dolan, S. Noda, S. Ui, T. Kudo, M. Ohkuma (2007)

3 Termite Gut Symbionts – W. v Egmond (2004)

5 A Dictionary of Genetics – R. C. King, W. D. Stanfield, P. K. Mulligan (2007) – Motility Symbiosis

6 Doing Biology – J. Hagen, D. Allchin, F. Singer (1996) – Chapter 3: Lynn Margulis and the Question of How Cells Evolved

7 Structure and Function of Cilia – Ciliopathy Alliance

8 Life: The Science of Biology – B. Purves, D. Sadava, G. Orians, C. Heller (2004) – Chapter 5: Cells: The Basic Units of Life

Review: How We Live and Why We Die: The Secret Lives of Cells by Lewis Wolpert

The jaw-dropping complexity and sheer cleverness of cells is beyond the imagination of anyone who has not specialised in the rapidly growing field of cell biology, and the pace and tone of Lewis Wolpert’s book How We Live and Why We Die: The Secret Lives of Cells reflect this. As a reader one cannot fail to be immediately awestruck by the sense of scale conveyed by Wolpert’s writing style, and the passion he has for the subject is apparent throughout the book.

The volume has fourteen chapters, each of which address a different aspect of how the workings of cells give rise to the phenomenon of life. Some rather advanced concepts such as development and cell signalling are discussed in a light-hearted, accessible manner. Wolpert often uses a humorous, anecdotal style, such as when recounting the bizarre etymology of the gene Sonic hedgehog: the biologist who named the gene did so after one of his son’s computer games due to the fact that a mutation in the gene causes fly larvae to have “a hedgehoggy appearance”. Analogies are also used in places – for example, positional values are explained with reference to the French flag.

Chapters towards the end of the book focus on the causes of cancer and other diseases on the cellular level, and are highly informative on these more sensitive topics. There is finally a chapter on the evolution of the very first cells, that is to say, the origin of life on Earth, and describes several theories to address this ultimate question, including the Miller-Urey experiment and the RNA World hypothesis.

As an introduction to the exciting area of cell biology, this book more than fits the bill: I found it to be a highly enjoyable read as well as packing a lot of information and presenting it in a fashion which allows the book to be read by those with little previous knowledge of biology. 

The Science of Allergies

In my last post, which was about how and why the cells within our bodies communicate amongst each other, I used the example of our immune system. This incredible network of white blood cells guards our bodies against disease-causing microorganisms with a variety of defensive mechanisms; the importance of our immune system is reflected in the disastrous consequences of deficiency diseases such as AIDS. Without an immune system, a common cold would kill you. The whole system relies on the fact that our white blood cells recognise pathogens as foreign, and thus set off an alarm signal which triggers the whole response – including the familiar symptoms of coughing, fevers and inflammation. As amazing as it is, the immune system is not infallible, and often can be set off by harmless substances which happen to find their way into our bodies – resulting in an allergic reaction.

When an allergen enters your body (which may be from eating it, breathing it in, or via the bloodstream, e.g. insect bites), it will bind to specific receptors on white blood cells – this happens because of their complementary shape. These cells will then send out signals which trigger the production of a type of antibody called Immunoglobulin E, or IgE¹. IgE then goes and attaches to another type of white blood cell called mast cells². The next time that allergen comes along, it will bind to the IgE antibodies, which once again have a specific shape which allows them to recognise the invading substance³.  The binding of the allergen causes IgE to change shape, kicking into an action a signal transduction pathway which causes the mast cells to release chemicals such as histamine⁴.

The effect of these chemicals is to induce the well-known allergy symptoms: in nasal allergies (collectively known as allergic rhinitis⁵), such as hay fever, histamine causes inflammation, sneezing, running nose, etc. but some allergic reactions have more serious effects. Anaphylaxis, for example, can be brought on by an allergy to nuts or insect venom; characterised by symptoms such as rapid swelling and hives, anaphylaxis can be fatal if not treated⁶.

So essentially, your immune system does a great job of protecting you from nasty bacteria, viruses and fungi, but every so often it gets it wrong, going into overdrive at the first sign of something harmless like pollen or pet hair. In a sense, it’s the price that must be paid for having a really good immune system; so while hay fever can be a real nuisance and many allergies can be very harmful, it’s a lot better than not having a working immune system at all!

References

1 http://www.scientificamerican.com/article/what-function-does-immuno/

2 http://www.worldallergy.org/professional/allergic_diseases_center/ige/

3 http://health.howstuffworks.com/diseases-conditions/allergies/allergy-basics/allergy2.htm

4 http://www.mastcellaware.com/about.html

5 http://www.webmd.com/allergies/tc/allergic-rhinitis-overview

6 http://www.medicinenet.com/anaphylaxis/article.htm

The conversations of cells

Imagine fifty people trying to build a house, only none of them can speak to each other or converse in any other way. The fifty people are all working towards a common purpose, but without any communication, their endeavour is bound to fail!

Instead, the workforce must cooperate in a highly organised manner. Firstly, they should be divided into groups, each with a particular purpose: laying the bricks, making the measurements, collecting and transporting the necessary resources, and so on. Yet even between these groups there must be communication: the brick-laying team could run out of cement, and would need to call on the resource-collecting group to obtain or make some more. With a clearly defined organisational system, it can now be hoped that the task in hand will be completed.

The very same is true of the cells in our bodies. Our cells are accumulated into tissues; several types of tissue make up one organ; and multiple organs that work together to ensure one aspect of the body’s functioning make up an organ system. Organ systems include the circulatory system, the nervous system and the digestive system.

Like the workers in the house analogy, cells must converse all the time, and they do so in a language consisting largely of proteins and lipids. These chemical “words” must be picked up and recognised without fail, and they must specify a particular response – though this response may be different in different cell types. Our cells have a very impressive vocabulary and, between them, can understand and respond to many thousands of chemical messengers. How does it work?

The entire process is based on two simple but absolutely fundamental principles in biology. The first is that two molecules will only piece together if their shapes allow one to fit into another, like a key into a lock. The second is that proteins, enormous molecules which regulate pretty much every process in our bodies, are very flexible in structure and the binding or unbinding of one substance will cause it to change its shape.

Take, for example, what is known as a protein kinase cascade. A messenger from one cell may fit perfectly into a receptor on another. The receptor, a protein, will then change shape, allowing it to bind other proteins and add a chemical group to them, so that these proteins in turn will change shape, and so on and so on. An important feature of this cascade is that the message is amplified at every stage, in the sense that every protein, once activated, will activate many more. It is like when a rumour is spread – one person tells several people, each of whom tells several more, and before long, everyone knows!

The message takes its effect when a final activated protein binds to DNA in the cell, thus altering the way the cell behaves in some way. For instance, the message could cause the cell to divide rapidly, creating many clones of the same cell. This is often the case when our immune system responds to an infection: the bacteria or viruses which cause the illness carry particular proteins which may enter our own cells, and hence be recognised by white blood cells because of their specific shape. The white blood cells divide, kill the bacteria or viruses, and send out signals which are recognised by other types of white blood cells. This second class of white blood cells, once activated, divide into many copies and begin making antibodies, which fit perfectly into the proteins on the bacteria or viruses and hence allow them to be destroyed.

The field of cell signalling is concerned with understanding exactly how cells make sense of the multitude of chemical messengers around them, and exactly how these chemicals cause the specific responses they are intended to trigger. It is an expanding field and one which I find fascinating. I hope you will also be interested and eager to learn more!

References:

Life: the Science of Biology – Purves, W.K; Sadava, J; Orians, G.H; Heller, H.C

The Biochemistry of Cell Signalling – Helmreich, E.J.M.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782684/

Industrial enzymes

Why enzyme biotechnology is increasingly important for modern industries

Many people may be vague about the actual definition of “molecular bioscience” and what it does for the community. A prime example of biomolecules being used in our day-to-day lives – both on a domestic and an industrial scale – is enzymes.

What are enzymes?

Enzymes are biological catalysts: proteins, made in the cells, which speed up all the chemical reactions inside all living organisms. They do this by binding to substrates (chemicals involved in a metabolic reaction) and lowering the activation energy needed either to build them up into larger molecules, or to break them down into smaller ones¹.An example of an enzyme-based reaction is the breakdown of starch into glucose by amylase enzymes in the saliva.

The part of an enzyme which binds to a substrate is called its active site. The active site is very specific in structure and will only bind to a particular substrate – a bit like a key fits into a lock (in fact, this is known as the “lock-and-key” model²). Because of this, living organisms need a vast number of different enzymes – one for every chemical reaction that takes place inside the body!

Why are enzymes used so much in industry?

The use of enzymes for manufacture goes back to about 8,000 years ago³ – when humans first used yeast to ferment grapes into alcohol. In the absence of oxygen, the yeast enzymes would break down glucose into ethanol and carbon dioxide. This batch process for the production of ethanol is still used today. At the time, of course, there was no understanding of enzymes and this was merely experimental. However in modern days, as our understanding of molecular biosciences and biotechnology has improved, we have been able to exploit the properties of enzymes to use them quite diversely.

Enzyme biotechnology really took off in the 1950s. Examples of enzymes used in industrial processes include:

·         Sucrase enzymes in soft-centred chocolates

·         Proteases and lipases in baby food to start pre-digestion

·         Biological washing powders to break down stains into soluble amino acids/fatty acids

·         Pectinase in fruit juice to increase yield and make the juice clear

·         Yeast enzymes in the fermentation of sugar

·         Rennin used to coagulate cheese

·         In the textiles industry to enhance the preparation of cotton⁴

·         Esterase enzymes to remove adhesives for the recycling of paper

The list really does go on. Enzymes as a form of biotechnology are growing rapidly: Figure 1 shows the projected growth of the global industrial enzyme market up to 2015. Why are enzymes so attractive to industries?

Global industrial enzymes market, $ millions5	Estimated value in 2010	Predicted value in 2015	% increase
Technical enzymes	1000	1500	50
Food and beverage enzymes	975	1300	33

Figure 1: the global industrial enzymes market is expected to increase at a compound annual growth rate of 6%

The use of biological catalysts to speed up industrial reactions is often favoured over the use of metal catalysts for two main reasons.

Firstly, enzymes operate at fairly low temperatures and pressures, which keeps costs down. Typically the temperatures required by enzymes are about ten times lower than those required by inorganic catalysts! In addition, enzymes can be up to 10,000 times more efficient than ordinary chemical catalysts, so profit is maximised.

What are the drawbacks of enzyme biotechnology?

Figure 2: enzyme activity increases

 with temperature up until the 

optimum – then it denatures.⁶

Okay, so enzymes aren’t 100% ideal – there are drawbacks to using them. The main one is that the 3D structure of enzymes is so fragile and thus largely sensitive to changes in temperature and pH. Figure 2 shows a graph of enzyme activity against temperature. As with all chemical reactions, the rate of an enzyme-catalysed reaction increases with temperature – up to a point. The polypeptide chains in proteins are held together by weak intermolecular forces (known as van der Waals forces and hydrogen bonds). At a certain temperature – often around 42⁰C – these weak forces are overcome and the structure of the enzyme’s active site changes. This means that the substrate can no longer bind to the enzyme, which is now said to be denatured. Denaturation is an irreversible process, so industries must regulate temperature very carefully. Note from Figure 2 how the optimum temperature of an enzyme (the temperature at which it has the highest rate of activity) is just below the point where it denatures – about 37⁰C. There is a very fine balance to be struck, therefore, between increasing the rate of a reaction and not permanently denaturing the enzymes which are catalysing it.

Sharp changes in pH also cause the denaturation of enzymes because functional groups in the active sites can lose hydrogen ions in a solution which is too alkaline and gain them in a solution which is too acidic. This means that the substrate can no longer bind to the active site. Different enzymes have different optimum pHs and so this can be harder to control than temperature.

Other issues which arise are the cost of extracting enzymes and the difficulty in reusing them. Enzymes are usually extracted from micro-organisms which are grown economically in bulk fermenters⁷. However, this is not a cheap process, and because enzymes are combined with substrates in an aqueous solution it can be costly to separate and reuse them as well.

Since the 1960s⁸ industries have employed a technique which resolves all of the aforementioned problems: immobilisation. By this method, the enzymes themselves are trapped in an insoluble material such as fibrous polymer mesh, and packed into a column through which the substrate can be continually fed. There are numerous advantages to immobilising enzymes:

·         The enzymes are more stable, so they are less likely to be denatured. This also means that higher temperatures can be used, increasing the rate of reaction.

·         The enzymes can easily be recovered and reused, making immobilised enzymes a more cost-effective method.

·         The enzymes do not have to be removed from the product and do not contaminate it.

·         Since the products are separated from the enzymes, there is no “feedback inhibition” – where products bind to the active site and prevent more substrates from reacting.

However, another issue of the application of enzymes cannot be addressed by immobilisation. In the 1970s evidence arose that proteases used in biological detergents could break down keratin in the skin and lead to skin irritation⁹. Although this has not been scientifically proven many people claim to have skin sensitive to biological detergents.

Enzymes in the future?

Over time, the use and efficiency of enzymes in industry has increased rapidly and they are now used in a diverse range of industries, from textiles to tendering meat¹⁰. Of course, there is still room for development and as research continues into how the efficiency of enzymes can be improved, enzymes will be put to new uses and new ones will continue to be discovered¹⁰. A current area of research is into enzymes which can withstand greater extremes of temperature, which would be particularly desirable in laundry and industrial processes where high temperatures are needed.

Who knows what developments the future will bring; however, it can be said with reasonable certainty that the enzyme industry is one which will continue to grow and develop.

References

1.  Life Study: A Textbook of Biology by D. G. Mackean
2. A2 Level Chemistry: The Revision Guide (CGP)
3. http://www.absorblearning.com/chemistry/demo/units/LR1507.html
4. Enzyme Biotechnology in Everyday Life by Theresa Philips
5. http://www.bccresearch.com/report/enzymes-industrial-applications-bio030f.html
6. http://www.rsc.org/Education/Teachers/Resources/cfb/enzymes.htm
7. www.spolem.co.uk/worksheets/docs/industrial_enzymes.doc
8. Carrier-bound Immobilized Enzymes: Principles, Application and Design
9. New GCSE Biology by Gemma Young and Sarah Jinks
10. http://prof.dr.semih.otles.tripod.com/enzymesused/enzymesused.htm
11. 11. Semih Otles, Professor of Food Chemistry

What's new in biology? Nanoparticles allow carefully timed cancer drug delivery

A couple of months ago I wrote my first post on the topic of biomaterials, in which I touched on the use of nanoparticles in medicine. Now a recent piece of a research has caught my eye on IFLScience: http://www.iflscience.com/health-and-medicine/nanoparticles-give-tumors-one-two-punch-timing-drug-delivery

How cool is this?! Here we have two drugs which, when taken together, will attack tumour cells: erlotinib slows the growth of the cell, and doxorubicin damages the cell's DNA and prevents essential cell processes, leading to its death. The drugs have been shown to be more effective when delivered with a carefully measured time delay. And how do they discriminate between healthy cells and cancerous cells? Simple: the drugs are delivered by nanoparticles called liposomes which bind to folate receptors on cancer cells, causing the liposome to break down. The first drug is thus released into the cell, where it primes the cancer cell for the second drug, which is administered in the same way 4-24 hours later. Experiments on mice have shown that this time delay is significantly more effective than taking the two drugs at the same time.

This is a pretty big leap in cancer treatment and one of the great things is that the nanoparticles have such specificity that they can target tumour cells over healthy cells. Applications of nanotechnology are everywhere, really.

The misleading use of language

One of the banes of science is that the way we use the English language often gives rise to misconceptions about scientific facts, giving people the wrong idea about how things work. I have found that it is often the case, when studying science at school, that these ideas have to be “unlearned” and replaced with the actual science. Here are eight particularly popular examples, many of which are favourites among my own science teachers.

1.       “Close that door – you’ll let all the cold in!”

A consequence of the second law of thermodynamics is that heat naturally flows from higher temperatures to lower temperatures. So in fact, by having the door wide open when it’s below room temperature outside, you’re not letting “cold” into the house, you’re letting heat out. “Cold” isn’t a tangible thing, it’s just a lack of heat; if you were to touch a dirty surface, you wouldn’t say that you were transferring cleanliness from your hand to the surface.

2.       “You’ve got a cold? Here, have some antibiotics!”

This one is a favourite of my Biology teacher’s (is favourite the word?). The same goes for a cough. The common cold and cough are viral infections – no amount of antibiotics will cure them, because antibiotics only target bacteria.

3.       “There are an almost infinite number of stars in the universe!”

This idea of “almost infinite” being a synonym of “an extremely large number” is one that I’ve even read in Biology textbooks. In the case of the stars, no-one’s denying that there are an enormous number of stars in the universe – more than we can imagine. Well, now think about how many atoms there are in the universe. If you think too long, it’ll make your head hurt – I mean, just think of how many atoms are in a single star. Stars are made of hydrogen and helium; a single gram of hydrogen contains over 600 billion trillion atoms, whilst a gram of helium contains more than 150 billion trillion. That’s not even to mention all the atoms present in planets like our own, as well as comets and meteors. Clearly, the number of atoms in the universe is many, many orders of magnitude greater than the number of stars – but it’s no closer to being infinite! Conversely, if you believe that the universe is infinitely large, then there may well be infinitely many stars (and atoms). But there is a clear distinction: a number is either infinite, or it is not. There is no crossing bridge between the finite and the infinite; you can never reach infinity by continually adding one. Thus there can be no concept of “almost infinity”.

4.       “I’ve got a respiratory condition.”

Breathing and respiration are completely different processes and it does little to help the situation that breathing disorders are called “respiratory conditions”. Breathing is the physical process of ventilating the lungs, taking in oxygenated air and expelling deoxygenated air. Respiration, in contrast, is a biochemical pathway in which glucose is metabolised in the presence of oxygen to carbon dioxide and water, releasing energy. (There’s more to come on breathing and energy!)

5.       “Maximum luggage weight: 20kg”

This is one we are bombarded with all the time, and again it simply boils down to how we use the English language. Kilograms, stones and ounces are not units of weight – they are units of mass. Weight is the gravitational force that is pulling you towards the centre of the Earth, and is measured in Newtons. As long as you stay on Earth, your weight will remain directly proportional to your mass (one kilogram corresponds to around 9.8 Newtons). However, if you went to the moon – or even further afield – where the size of the gravitational field was different, your mass would not change, but your weight would.

6.       “Black surfaces absorb heat.”

This isn’t scientifically inaccurate, but it can lead to some confusion about cause and effect. It is not the case that, because a surface is black, it therefore absorbs heat – in fact it is more like the opposite. A surface which absorbs all wavelengths of visible light, as well as infrared (heat), will not reflect any visible light (or at least very little) and will consequently be black.

7.       “We breathe oxygen in and carbon dioxide out.”

This makes it sound like our breathing system has some sort of filter, which only lets oxygen in one way and only lets carbon dioxide out the other. When we breathe in, we create a pressure gradient that forces air – containing nitrogen, oxygen, carbon dioxide and small amounts of other gases – to enter the lungs. Oxygen then diffuses from the lungs into the blood, so that it can be used for respiration; whilst carbon dioxide, produced in respiration, passes from the blood back into the lungs. The air is then expelled from the lungs thus has a lower concentration of oxygen and a higher concentration of carbon dioxide than the air that was inhaled, but it is still a mixture of the original gases. Breathing is necessary in order to maintain a concentration gradient between the lungs and the blood.

8.       “We respire to make energy.”

This is an old one, and we’re back again to the good old laws of thermodynamics. Energy can’t be created or destroyed – it can only be transferred from one form to another!

Book review: Seven Clues to the Origin of Life by Alexander Graham Cairns-Smith

I found this book while doing research for my Extended Project, the focus of which is the RNA World hypothesis and the Miller-Urey experiment. By the time I got to the end of the book, I was convinced that neither of these were plausible explanations for the origin of terrestrial life, because Alexander Graham Cairns-Smith had utterly persuaded me that his own hypothesis was correct.

Seven Clues to the Origin of Life presents the argument that the first molecules of life were assembled on clay, which provided a template on which inorganic crystals could self-replicate. Despite the fact that there is ingenious science within the pages of the book, I found it light-hearted and enjoyable reading which was accessible for all as well as gripping. The book assumes very little prior knowledge of chemistry and biology, with the first couple of chapters introducing some fundamental principles and discussing the molecules of life. The whole thing was narrated in a detective novel style, with quotes from the original Sherlock Holmes books by Conan Doyle at the start and end of each chapter; and the intelligent use of analogies to illustrate core concepts was excellent. In particular, I liked the “scaffolding” idea, illustrating how seemingly interdependent, complex processes could have arisen from simpler building blocks, some of which were later removed. I appreciated the escape from the logic that, since nucleic acids and proteins are interdependent in today’s cells, the first organisms must have been based on RNA, as I just don’t think the random synthesis of active RNA molecules under prebiotic conditions is really plausible (again, Cairns-Smith cleverly argues this by comparing it to the probability of rolling a million 6s on a dice in a row).

The hypothesis itself was a courageous one, deviating largely from most of the current theories mainly in that it suggests that the first life forms were inorganic. Concepts such as supersaturation and self-assembly are explained with clarity and detail, while still capturing the reader’s excitement as the picture is gradually built up, describing how crystals could have formed and replicated on clay surfaces and hence acted as genes, with errors in replication leading to “evolution by direct action”.

The core theme of studying the most perplexing features of a case in order to crack it is well maintained throughout, making for enjoyable reading as well as learning. I found Seven Clues to the Origin of Life a superb book, one that should be read at the very least by anyone with an interest in the chemical origins of life, and preferably by anyone with an interest in chemistry and biology.

The Evolution of Science Journalism?

This is part of an OpenSciLogs/Indiegogo project entitled “the History of Science Journalism” to which I contributed. To add your own contribution go to: https://docs.google.com/document/d/10hB4Pa1Alx-m04iON9-QfKOSp3kfCpRENeN-vFC0Ft0/edit

When asked what I want to do in the future, I reply, “science journalism”. The most common responses I get are “what’s that?” and “ooh, haven’t heard of that one before!” One person remarked: “science journalism? Those are two words I’d never have put together!”

Does this mean that science journalism is dead? I should hope not! I think it is simply the case that people aren’t used to hearing the term – after all, it is commonly assumed that science graduates have one of three broad career options: academic research, teaching, and medicine. Yet the public is exposed to science journalism, in the form of documentaries and news headlines. Science is what informs society about stem cell research, newly discovered drugs, new materials.

Clearly, the way in which we receive science news is diversifying: the use of blogs and social media is taking over, with more traditional forms of journalism becoming less popular. Wanting to know whether and how the content of science journalism has evolved, I decided to look through the Archive of the Popular Science magazine and gather some statistics.

I selected a random issue (two issues at the start, when they were short) from every 4^th year between 1872 and 2008 and counted the number of articles which best fit into 12 broad categories (this took longer than expected!) and got some interesting results:

Articles in the “other” category initially consisted largely of history and philosophy of science, but later these were replaced with advertisements, readers’ opinions and economics.

Far be it from an aspiring science writer to attempt to draw conclusions about the evolution of science journalism from just one magazine – that is not how the scientific method works! – but there were several points of note from the Popular Science archive:

·         For the first 40 years or so, each issue comprised around 10 long, research-paper style articles about developments in science. These were broad in topic, but with some preference for the biological sciences and a lot of articles focusing on sociology, anthropology and philosophy.

·         At this point there were relatively few articles on engineering and technology, with the odd paper on electronics and mechanics.

·         1916, right in the middle of WW1, was the first major turning point: the magazine became more newspaper-style, with many more articles which were much briefer; the focus at this point shifted almost entirely to new inventions and machinery, which continued to dominate the magazine. From then on there was hardly any mention of physiology, psychology or philosophy.

·         It was interesting to note some important scientific discoveries which nonetheless were not front-page headlines and could easily have been missed. For example, June 1948: “Experiments prove you can’t destroy energy”.

·         In the 40s and 50s there was a big increase in home and DIY, with entire sections devoted to this.

·         From the 80s onwards there began to appear articles on renewable energy sources and mention in advertisements of products being eco-friendly, suggesting this was around the time we began to become self-aware of our impact on the environment.

To what extent does the coverage of science in the media affect the direction of scientific research? I think this is especially the case with somewhat controversial current topics such as GM and stem cell research. These are big scientific advances, but they raise ethical issues and it is important that scientists take public opinion into account. However, I also think that science journalists should stress where possible that the benefits of these advances often outweigh the moral issues. For example, many people argue that the creation of human embryos in stem cell therapy is akin to creating and then destroying a potential human life, but a sense of perspective is needed here, i.e. many lives will potentially be saved; furthermore, can an embryo really be likened to a human life? I’m currently reading How We Live and Why We Die: The Secret Lives of Cells by Lewis Wolpert, in which developmental processes in humans are discussed. With all the massive changes, including cell division, differentiation and the formation of organs, that the single fertilised egg must undergo before it even resembles a human being, Wolpert argues that it is not justified to allocate the same rights to an embryo that one would to a human.

What would I like to see in the future with regards to science reporting? I’d like the relationship between science news and the public to be more two-way, more interactive. With the increase in social media for reporting scientific news and discoveries, I can envisage a situation where more people become engaged in the news they receive - give feedback, ask questions, push for more information. Now that would make a science journalist’s job very interesting, in my opinion.

The data came from http://www.popsci.com/content/wordfrequency#internet.
The project "the History of Science Journalism" belongs to Robin Wylie, PhD student. Please feel free to contribute to the document.

“Give me more chocolate!” (An Easter special)

Ever since the dawn of chocolate in Mesoamerica almost 4000 years ago, it has been no secret that the stuff makes you feel good. Chocolate was first drunk as a beverage by the Olmec people of Mexico around 1900BC¹, possibly for medicinal purposes. It remained native to South America until the 15^th century, when it eventually spread to Europe. By this time people valued chocolate so much that cacao beans were used as currency!

Nowadays, needless to say, chocolate is a big hit worldwide: the average British person consumes 10.2kg each year², and the figure is higher in Switzerland, Belgium, Germany and Ireland. Today being Easter Sunday, no doubt many of us will be shamelessly tucking into chocolate eggs. What is it about this delicious treat that makes us tick?

To quote the beloved fictional chocolatier Willy Wonka: “Chocolate contains a property that triggers the release of endorphins. Gives one the feeling of being in love.” The active ingredient to which Wonka is referring, known as theobromine³, does indeed cause the brain to secrete these feel-good hormones, and is regarded as the main reason why eating chocolate makes us feel great. Chocolate also stimulates the production of serotonin⁴, a chemical which boosts happiness.

A further ingredient in chocolate, anandamide, has been shown to work by activating the same brain region as the active ingredient in cannabis⁵. But don’t panic – that doesn’t mean eating chocolate will make you high! The levels of anandamide in chocolate are considered too low to have a noticeable effect (unless you were to eat several pounds of chocolate – not advisable!)

Our brain’s reward pathway system can also be held accountable. What is the reward pathway system, I hear you ask? Certain things necessary for our survival trigger a rewarding feeling in our brain, a system which has evolved to help us to survive and reproduce by motivating us to repeat the action as often as possible. Sex is one example: essential for us to reproduce and pass down our genes, sex stimulates a pleasurable feeling which makes us want more. Eating has the same effect, and energy-rich foods such as chocolate trigger the pathway more than others⁶ (I for one don’t find that brussel sprouts have this euphoric effect).  

Apart from improving our mood, chocolate has been shown to have numerous health benefits (in moderation, of course). For example, chocolate can reduce the risk of heart disease by lowering cholesterol levels in the blood³, and also replenishes minerals such as magnesium⁴, restoring the body’s optimal function during menstruation, for example. These health benefits are greater in chocolate with a high percentage of cocoa. Furthermore, it has been shown that the link between chocolate and acne is merely a myth³ (phew!).

Before concluding, I feel obliged to add that the above does not mean we should all stuff our faces with as much chocolate as we wish all the time – the sugar and fat content can of course lead to problems such as diabetes and obesity – however, perhaps it will make you feel less guilty about indulging yourself at this festive time of year. On that note, I wish you readers a very happy Easter, and please, comment away!

1.       http://en.wikipedia.org/wiki/History_of_chocolate

2.       http://www.exportsolutions.com/ExportTipsDetails.aspx?id=74&title=Fun

3.       http://www.purdys.com/Facts-About-Chocolate.aspx

4.       http://www.medicalwellnessassociation.com/articles/chocolate_benefits.htm

5.       http://edition.cnn.com/HEALTH/indepth.food/sweets/chocolate.cravings/

6.       The Biochemist, Vol.35 No 6, Gluttony (p4-9)

Image credit:

http://wodumedia.com/wp-content/uploads/2012/11/The-spun-sugar-boat-makes-it-way-down-the-chocolate-river-in-Warner-Bros.-Pictures-fantasy-adventure-Charlie-and-the-Chocolate-Factory-starring-Johnny-Depp.-Photo-courtesy-of-Warner-Bros.-Pictures-17-960x518.jpg

http://zerowoes.com/wp-content/uploads/2014/04/chocolate15.png

What’s so special about water?

Of all the many mysteries of the living world, one particular puzzle stands out to me. With the enormous range of organic compounds with complex structures and functions that are found in living organisms, how can it be that the most important, and most unusual, compound in life consists of two hydrogen atoms attached to an oxygen atom?

Water is a functionally diverse molecule which, as we all know, makes up about 70% of our bodies. Certain bizarre properties are unique to water and enable it to act as the molecule on which all life as we know it is based. Why should this be?

First, we should look at the chemical and physical properties of water molecules. The distribution of charge in the molecule means that the oxygen atom is ever so slightly negative (δ-) and the hydrogen atoms are slightly positive (δ+). Because opposites attract, two adjacent molecules are attracted to each other by these opposing charges. This attraction, known as the hydrogen bond, is enormously important and accounts for most of water’s counter-intuitive properties.

Armed with this, we can now look at what it is that makes water so special. Hydrogen bonding explains why, for example, water is liquid at room temperature, while most very small molecules are gases. The state a substance occupies at room temperature is all to do with how well its particles are held together: the more they are attracted to each other, the more energy will be needed to separate those particles, and hence the higher the melting and boiling points. If water were a gas at room temperature, or at 37^oC, the temperature of our bodies, life would not be able to use it and we would not exist.

The majority of substances are denser in the solid state than as a liquid, but if you put an ice cube in a glass of water, it will float, in the same way that icebergs float on oceans. This tells us that somehow, water molecules are closer together in liquid water than in solid ice! Our old friends the hydrogen bonds are once again to thank for this property: ice occupies a regular crystal structure with hydrogen bonds holding water molecules at a fixed distance apart, a distance which is greater than that between molecules in liquid water. 

What is the significance of this property? To cite one example, notice that at temperatures below 0^oC, ponds freeze from the top down, rather than from the bottom up, owing to the fact that ice floats. However, the ice on top insulates the water below, which remains liquid. If ponds froze from the bottom up, all the aquatic animals and plants would die because the entire body of water would freeze up!

The fact that water molecules stick so well to each other (the scientific term is cohesion) allows a remarkable phenomenon to take place in plant stems: water can be transported relatively long distances up the stems of plants against the force of gravity – all because of the cohesion between molecules. When water evaporates out of the leaves, water at the top of the stem is pulled upwards, creating tension on the water in the stem. This is appropriately known as the “cohesion-transpiration theory”, and plants could not live without it because they could not get water to their leaves for photosynthesis, among other things.

I will conclude with two further properties of water that are important at the cellular level. Water is special in that it is an excellent solvent of many substances: salt, for example, will dissolve if you add it to a glass of water. In cells, this means that glucose, ions and other things can easily be transported round the body by water in the blood. In addition, water is so small that it has no problem in passing through the membranes of our body cells, which act like filters to keep out unwanted substances.

I hope this was interesting and valuable, and please feel free to comment with any feedback. My next post, in a fortnight’s time, is likely to be related to Easter: I’m thinking of writing about the biochemical effects of chocolate on the brain and body, so stay tuned!

References:

Life, the Science of Biology (Seventh Edition) – W. Purves, D. Sadava, G. Orians, H. Heller

New Scientist, issue 2746 p33-35: The strangest liquid: why water is so weird                           

Images: http://www1.lsbu.ac.uk/water/ice_iv.html

http://www.studyblue.com/notes/note/n/chapter-2-water-and-carbon-the-chemical-basis-of-life/deck/104681

What do our cells and hydroelectric power stations have in common?

If you go to Dinorwig, a small village in North West Wales, you will see an incredible feat of engineering. Below Elidir mountain, 16km of tunnels¹ make up a hydroelectric power station with an approximate output of 1,728 megawatts². How is this electricity generated?

A dam is used to store water in Marchlyn Mawr reservoir; the underground tunnels allow water to flow downhill into Llyn Peris reservoir, turning a turbine which generates the electricity in doing so. But Dinorwig power station is not just any old HEP station: it uses pumped storage, a method where off-peak, cheaper electricity is used to pump water back up from Llyn Peris back up to Marchlyn Mawr, so that it can be reused³.

Dinorwig power station is one of only two pumped-storage hydroelectric power stations in the UK (the other one is in Ffestiniog, also in North West Wales). But a very similar system exists at all times in the cells of every single living organism: chemiosmosis.

When we respire, we break down glucose in the presence of oxygen to release energy, which can then be used to drive processes in our cells. This actually takes place in a large series of chemical reactions which occur in the mitochondria (the “batteries” of living cells). In the final step of this process, electrons are passed through a series of protein complexes, releasing bursts of energy that can be used to pump hydrogen ions from the interior of the mitochondria to the space between its two membranes. In this stage, the ions are being pumped from a lower to a higher concentration (naturally they would move from higher to lower without the input of energy). This is analogous to the pumping of water from the lower reservoir to the higher reservoir, using energy to drive the water against the force of gravity.

The hydrogen ions in what is known as the intermembrane space now have potential energy in the form of a concentration and charge gradient. Our cells can make use of this energy: as the ions flow passively back from the intermembrane space into the interior of the mitochondria, the energy from their movement is used to produce a molecule called ATP, the energy currency of our cells.

To me, chemiosmosis is just one illustrator of the fantastic machinery of our cells and bodies. It never ceases to amaze and dumbfound me how complex even the most primitive of organisms are, and how evolution by natural selection has shaped the biological processes that occur within our cells all the time without us even thinking about them. I hope you find this as interesting as I do, and if you didn't already know about the chemiosmotic mechanism, then perhaps you've learnt something new.

I haven’t decided what my next blog post will be about, but it could be on either eusocial behaviour or the biological significance of water. If you’re reading this, I would really love feedback and ideas, just so I know that I’m reaching people! Thanks a lot.

References:

1.       http://www.fhc.co.uk/dinorwig.htm

2.       http://en.wikipedia.org/wiki/Dinorwig_Power_Station

3.       http://water.usgs.gov/edu/hyhowworks.html

4.       http://www.fhc.co.uk/images/pics/dinorwig1.jpg

5.       http://84d1f3.medialib.glogster.com/media/d6/d613b845a769d565f901820c957de1a0bd2b2acf866f291d636a3e60fb648295/co-jpg.jpg

Biomaterials: applying materials science to living organisms

So, I decided to focus my first proper post on biomaterials. Biomaterials science – there’s a field which unites the three sciences if I ever saw one. Materials science hovers delicately on the border between Chemistry and Physics, and here materials are exploited for use in living organisms, with obvious medical applications.

Biomaterials science first grabbed my attention when I was at a materials summer school at Manchester University, and there was a research talk on it which really interested me. I find it fascinating that scientists can engineer materials that can be used to improve the way our bodies work in some fashion. And the applications are so diverse: from the tiny buckminsterfullerene (buckyballs) which can be used in drug delivery, to the design of prosthetic limbs¹ – the possibilities are enormous.

   A carbon buckyball can transport drugs 
         to particular cells in the body²

An important type of biomaterial is nanoparticles – substances which are less than one ten-thousandth of a millimetre in length or thickness. Being so tiny, nanoparticles can enter our cells and move through blood vessels. A particular application of this that I’ve been reading about is gold particles in biomedicine.

One use of these gold particles is in chemical delivery systems: the nanoparticles are bound to or coated with a substance that you want to introduce into the cell (such as a particular protein)³. They are then “engulfed” by the cell: the membrane of the cell pinches in and fuses around the gold particles, a process called endocytosis. The substances attached to the gold particles are targeted at a particular part of the cell, such as the nucleus (the information-containing centre of a cell), but doing so has proven difficult because after the particles have been taken into the cell, they are often stuck inside the bit of membrane which originally engulfed them (known as the endosome)³. This is a big problem!

There are many other diverse applications of biomaterials which are rapidly growing, such as tissue engineering (where body tissues are regenerated or enhanced using cell exploitation techniques)⁴. I hope my rather superficial overview of what biomaterials is about has interested you as a reader and perhaps inspired you to learn more.

I’ll end my first post here; look out for my next one which *might* be on the chemiosmotic principle. Thanks for reading!

1.       http://science.howstuffworks.com/prosthetic-limb.htm

2.       Picture: http://www.animalnewyork.com/2012/la-dolche-vita-rats-fed-carbon-buckyballs-in-olive-oil-live-twice-as-long/

3.       The Biochemist, Vol 35. No 1. Gold Nanoparticles in Biomedicine by Catherine Berry

4.        http://www.tissue-engineering.net/index.php?seite=whatiste