Monday, 25 June 2007

Guest article: Economics...

As we struggle through the last exams of term, I thought that leaving the 'biology bubble' for a while could be a good idea... so I have invited Miguel Faria e Castro, a promising economics student at the faculty of Economics, Universidade Nova de Lisboa (New University of Lisbon) to bring a bit of fresh air to the blog...

When the invitation to write an article for this blog first came, I felt that anything written by an Economics student would feel a bit out of place. It happens, however (and most fortunately, in my own personal opinion) that Economic Science is not restricted to, as some people think, heavy statistical paperwork and impossible mathematical models with two thousand variables. A wide, varied field, it incorporates a lot of knowledge from other scientific subjects, namely psychology, sociology, physics – even biology!

It is not my intention to bore you with sophisticated technical terms or theories which are able to explain whether you opt for a cup of tea or a chocolate bar under the right conditions. That is why I have decided, in this brief article, to give you a first glance at what really is economic science.

Curiously, the term “Economics” comes from a very picturesque Greek expression: Oikosnomos, or, in plain English, “how to take care of your house”. Coined somewhere in the ideological turmoil of the 18th century, it came as a brief, yet clear, reference to the founding pillar of the entire science, the concept of scarcity: How can I satisfy my endless needs with the limited resources that are available to me? This is commonly known as the fundamental problem of economics, this is the problem that more or less 6 billion people face every day, at every moment.

Everything gets more complicated when we notice that not only people have different interests and, therefore, different needs, but also different qualities and quantities of resources available to themselves. This was what Adam Smith, a late 18th century Scottish philosopher who is commonly recognised as the first modern economist, attempted to analyse when working in his great (quite literally, three volumes of 1,000 pages each) work: The Wealth of Nations. Basically, the entire work was a defence of two fundamental economic theories, and I am almost sure you have already heard of at least one of them somewhere: The Invisible Hand, and The Division of Labour. While the former states that each individual, while attempting to prosecute his own self-interest will ultimately contribute to the society’s greater good (or, “after all, being greedy is not that bad”), the latter is based on the principle that certain countries appear to have a natural advantage on the performance of certain tasks over others, and that the entire world would gain if each country focused on what it’s good at. Another founding father of economics, the British David Ricardo would further develop this theory, by proving, with a simple mathematical example that it would be better for both countries if Portugal only produced wine and England textiles, rather than having them producing both resources. Look in wikipedia for “Comparative Advantage” and you’ll learn a neat trick with which to impress your friends (this last part sounds quite nerd, but we were actually told it by a professor).

As with every science, new theories on how to better satisfy people’s needs appeared. The so-called Classics, which I have just mentioned, tended to follow a very liberal orientation. Throughout the 19th and 20th centuries, economics, initially seen as a weird mixture of politics, law, philosophy and mathematics, increasingly became a matter of interest for politicians – the rise of Marxism as a political ideology only happened because Karl Marx had launched the theoretical basis for his own economic principles (usually called Marxian economics, as to avoid any embarrassing confusions). Until the 20’s, economic science focused almost exclusively on the behaviour of those who produced every day’s goods and those who bought it – Consumer and Producer Theory, the basis for what is today known as Microeconomics (it studied the individual behaviour of economic agents). In 1929, however, with the Great Depression, the Western “Civilised” World was hit, for the first time in History, with widespread inflation and unemployment. Two occurrences which, as the economists of that time conceded could barely be explained by the tools that they were using.

This is where another great mind enters. An Englishman named John Maynard Keynes – a brilliant thinker (the philosopher Bertrand Russell once said that Keynes was the most intelligent man he had ever met) and fierce investor who would publish his thoughts on what had happened during the Great Depression in the United States of America and the rest of the world. His work led to the creation of an entirely new field – macroeconomics, or the study of the aggregate behaviour of all economic agents (and now the State plays a special role…) when faced with certain circumstances and conditions. Keynes was the first to identify the fact that a phenomenon such as inflation (which is, by the way, the continuous and generalised rise in the price level or, in English, the occurrence thanks to which things are much more expensive today than they were when your parents were eighteen) could never be explained by studying what an individual consumer does or a single firm does not do. Only by studying the economy as a whole, can we grasp the real magnitude of such an event. A recurring joke about economists tells you that one of the advantages of being one is that, when you are in the unemployment line, you will at least understand why you are there. Thank Mr Keynes for enlightening you on that. But enough of history.

A common misconception is that economics only deals with money. Money is, as surprising as it may seem, a very small part of this grand show. Do you eat money? Do you drink money? Do you drive money? The answer is no – money is merely the means for you to get whatever you need. This is where we get at another important concept – the Classical Dichotomy, which basically states that real, not nominal, variable are important. What is the difference? Imagine you are a happy German with a monthly income of €5,000. Then, there’s that Polish guy who makes only €5 a day. It happens, however, that an apple in Germany costs €1,000 , while the Poles can eat them for €0,5 each. Which means that, nominally, you earn €5,000. But your real wage is 5 apples, while the Pole earns 20 apples a month. His real income is four times yours, even though you nominally earn a thousand times more. Interesting, eh?

Sunday, 24 June 2007

Guest article: Decision-making

Our guest writer this week (well, maybe this will become weekly) is Christina Ieronymides, student and aspiring thylacine hunter. Hailing from Cyprus, she has just completed her BSc in Zoology at Imperial College, and will be doing her MSc at the Institute of Zoology (London Zoo) starting this autumn. Without further ado...

As a guest writer on this blog I feel the need to point out that my grasp of genetics does not extend much further than the basics, and molecular biology, in fact, is one of the subjects I tend to steer clear of. This does not mean I dislike the field; it merely indicates that I may find myself in need of a molecular geneticist friend at some point in my career.

In this article I’d like to introduce a couple of my pet subjects. The nature-nurture debate is well known to most people involved in the biological sciences, and despite all the controversy, “a bit of both” is the answer. This gives rise to the phenotypic gambit: that there is a genetic element in animal behaviour, and as such what you see is behaviour that is adaptive and under selection. This is the basis of behavioural ecology, a field to which I was first introduced by Richard Dawkins in his classic work The Selfish Gene.

In his book, Dawkins uses game theory to look at the evolutionary outcome of social interactions between individuals adopting different behaviours, and more specifically to explain how cooperation can evolve amongst social conflicts. He explains how cooperation results in the best overall outcome for the individuals involved, when a win-win outcome is possible. Cooperation is, however, a fragile state, dependent on small population size, repeated interactions over time and communication. These conditions are vulnerable to outside influences, such as immigration, population growth and change in the social circumstances.

Externalities imposed on such a system of reciprocal altruism inevitably lead to the break down of cooperation. This is the root of the Tragedy of the Commons. Open-access resources are doomed to overexploitation because people only think in the short term, and this is what we see happening in the world’s fisheries today.

Achieving sustainable resource use is only possible in the light of the incentives that individual resource users face. In the case of the bushmeat trade, conservation, development and animal welfare collide. Overexploitation of tropical forest fauna for food has both biological consequences and consequences for people. This bio-economic system operates at a number of scales (from the decisions made by an individual hunter to consumer demands and the wider economy) and is dynamic and heterogeneous (species abundances and population dynamics within the forest), and is therefore particularly difficult to tackle.

Resource management is in general complex and policies put in place to ensure sustainability are usually unsuccessful, as conservation clashes with the human element. In many cases, it is necessary to convince the public that management is worth while. Scientists are generally quite poor at communicating their knowledge to the people they are serving. This lack of communication between science and the public carries much of the blame for the distrust towards science that we see growing among lay people. Laurie Marker’s work on conservation of the cheetah in Namibia is an excellent example of understanding the social, economic and biological issues and cooperating with the locals in such a way so as to introduce acceptable and effective solutions. Marker’s work highlights the fact that accessible information, education and the fostering of trust are paramount for the successful implementation of any resource management scheme or policy.

Friday, 22 June 2007

Why dream?

We all know what dreaming is, experiencing sensations such as images and sounds during sleep that we usually cannot control. Lucid dreaming is when the dreamer is aware they are dreaming and can sometimes alter their actions and the dream world. Anxiety is the most common felt emotion during dreams. Dreaming is associated with the REM (Rapid Eye Movement) stage of sleep. We go through ~4 cycles of REM sleep. All the muscles in our body are paralysed apart from the muscles in your eyes hence the name.

But why do we dream at all, nearly all mammals and birds appear to do it. Suggesting it must be evolutionary beneficial but how? Some people have thought dreams were messages from god or predictions of the future. Early psychologists like Freud were interested in dreams and their meanings. He believed dreams were wish fulfilment. Your unconscious mind doing things your conscious mind does not allow it when you are awake, but your ‘superego’ sensors your dreams. Part of this is symbolism, items and events represent what you really want. Freud has said not everything is a symbol, ‘sometimes a cigar is just a cigar’. He thought if you understand what they meant and resolve the deep arguments within yourself then all is well. I have never thought this made evolutionary sense…how many psychoanalysists were there in cavemen times to help them by charging +£60 to listen to them speak? Not many I would assume but I have no data on the matter.

Neuroscientists have also tried to explain why we dream. The great neurobiologist Crick (yes I do mean the on and only Crick) put forward the theory of reverse learning as a reason for why we dream. This theory says we dream to forget! The theory says we take in too much info in during the day so at night we erase these memories. Otherwise they would become damaging to you. This theory has little experimental support. It doesn’t explain why newborns sleep and spend so much time in REM (assuming they are dreaming). Also why do dreams have a story if they are simple a deleting mechanism? Why not simple flashes of sound and images, or has our brain come to make sense out of this, what function could that have. Lloyd et al. (unpublished) criticises it by showing more dreams are experienced when revising and yet much of the information stays. He suggests dreams are either a way of rehearsing or organising the information. But he fails to explain why dreams usually have little to do with what has been learnt. But it is clear information is not being forgotten.

Dreams have also been seen as a way of solving problems. Are you in fact thinking during dreams and coming up with ideas? This seems hard to grasp – you are actually thinking but have no control. Kekulé figured out the structure of benzene through dreaming of snakes biting its tail making a ring. Lloyd et al. also provides evidence of this. The subject woke up from a dream with the answer to chemistry homework that they were unable to solve beforehand. However there is no evidence people who do not pay attention to dreams have more difficulties in life than those who do.

It is hard to figure out what is going on with dreams, we cant figure out what memories are on the molecular level let alone how dreams arise and what function they have.

Just remember you do not know you are dreaming in non-lucid dreams then how can you prove you are not dreaming right now! (warning the devil is in me)

Friday, 15 June 2007

Hypothermia and paradoxical undressing

The temperature of our body is normally around 37ºC… however, it is only necessary a 2º decrease for hypothermia to initiate… As body temperature decreases even more the consequences become more and more negative, so that between 25 and 28ºC the heart just stops and dead is the logical outcome...

Considering that hypothermia is caused by a decrease in body temperature, how to explain that so many people are found dead due to this condition and yet with no clothes on? As this scenario was very often observed in poor people in cities, the logical explanation was raping and theft. Yet this doesn’t explain why victims of hypothermia refuse warming clothes when rescued… Overall, this phenomenon is commonly referred to as ‘paradoxical undressing’…

How to explain this apparently contradictory behaviour? A quite logical theory tries to give an explanation. When hypothermia initiates, the organism tries to prevent vital organs from cooling too much, and as a consequence the ‘available’ heat is concentrated to central areas of the body. This is possible by reducing peripheral circulation, namely by contraction of blood vessels. Vasoconstriction, possible by contraction of those muscles situated around blood vessels, requires energy, namely glucose provided by circulation itself.

Vasodilation, on the other hand, doesn’t require energy. Therefore, after a period of stress as that of hypothermia, with reduced income of energy and accumulated tiredness, the muscles lining the vessels tend to relax and allow once again the flow of blood into the restricted areas of the blody. The sudden flow of blood kept warm by its concentration elsewhere is thought to be responsible by the sudden sensation of warmth which leads hypothermia victims to undress. Obviously, the undressing turns out to help the hipothermial process, and victims eventually die. In fact, there is no register so far of any hypothermia victim able to survive without help after reaching the ‘paradoxical undressing’ state.

To finish off it is interesting to note that in 20% of the lethal cases of hypothermia another perhaps not so strange situation is registered, the so called ‘hide-and-die’ syndrome, which leads to the finding of hypothermia victims hiding in the most unlogical places, namely under beds of behind closets. This is probably the remains of an old instinct that seems to be present in a variety of animals and can basically be translated into the following piece of wisdom- ‘when things get really bad, find somewhere to hide’. I wonder if this works with the exams too… :-)

Based on ‘Paradoxical undressing; 21st April 2007, pag 50, New Scientist

Yawning makes you cool

ResearchBlogging.orgYawning is a semi-voluntary action performed by pretty much all vertebrates. It consists of three phases: a long inspiratory phase, a brief acme, and finally rapid expiration. This is accompanied by many physiological and neurological changes, such as muscular stretching, increase of blood flow and a sense of pleasure with dopaminergic activity in certain regions of the brain (Daquin et al., 2001). Yawning does not, as such, affect arousal in a physiological sense (Guggisberg et al., 2007), but it is obviously associated with boredom, waking up and feeling sleepy. As everyone knows very well, yawning is also contagious. This is not true just for humans, this is true for all social animals who have a sense of self-awareness (i.e. can recognize themselves in the mirror) (Perriol et al., 2006).

Why do we yawn? There are so many different changes associated with yawning that it could really be anything. Hippocrates considered it to be a mechanism for exhaustion of the fumes preceding fever. For the largest part of the 20th century, it was commonly thought that it was a mechanism for "balancing" oxygen and carbon dioxide levels, until this was shown to be untrue in 1987 (Provine et al.). There is obviously some connection with the states of sleep and wakefulness, but is that all? Also, why is it contagious? Is it just a mirror neuron driven response, or does it have a useful function?

The evidence for the connection between yawning and the sleep-wake rhythm is quite convincing. Even though this is generally common knowledge, Zilli et al. (2007) showed that yawning occurs more frequently in the early morning and late evening. Also, it was shown that evening-types (people who tend to stay up late, like myself) yawn more frequently than morning-types, showing that there is a connection between changes in the sleep-wake rhythm and yawning.

Another interesting connection is that between yawning frequency and REM sleep as observed throughout life. Humans can yawn from as early as 12 weeks after conception. Yawning frequency then very slowly declines with age. There is a very similar pattern in the amount of REM sleep, along with some physiological connections, such as the muscle stretching in yawning counteracting the muscular atonia seen during REM sleep (Walusinski, 2006).

The contagiousness of yawning is, for most people, its most interesting aspect. Anderson et al. (2004) showed that yawning is contagious in chimps, while Paukner et al. (2006) showed that the same is true in stumptail macaques. Infant chimps exhibited no yawning in response to the same experiments, which is in line with the evidence that human children under the age of 5 do not respond to seeing a person yawn like older humans do. Considering this and the fact that only animals with a sense of self-awareness exhibit contagious yawning, could contagious yawning have some connection with intelligence or social interaction?

Another aspect of contagious yawning is that it is correlated with interoception (sensitivity to stimuli arising within the body), self-awareness and empathy, as well as mental state attribution (the ability to inferentially model the mental states of others) (Platek et al., 2003). Functional MRI shows that brain activity correlated with contagious yawning is significant in the bilateral precuneus and posterior cingulate, regions highly associated with self-processing but, surprisingly, there is no activity in regions associated with mirror neurons (Platek et al., 2004). Yawning seems to circumvent the mirror neuron system, suggesting that yawning is an automatically released behavioural act and not an imitated motor pattern requiring detailed understanding (Schurmann et al., 2004).

most surprising data comes from a 2007 study by Gallup et al. which suggests that yawning is a mechanism for thermoregulation of the brain. The response of human subjects to videos of people yawning was observed. Subjects breathing through the mouth exhibited 48% contagious yawning, while subjects instructed to breathe nasally did not yawn at all. Nasal breathing is associated with brain thermoregulation by the cooling of the vertebral artery and the forebrain. Also, subjects with a cool compress applied to their foreheads yawned significantly less than subjects with no compress or a warm compress applied. This leads to the formulation of an interesting theory with testable predictions about the thermoregulatory function of yawning based on the rapid intake of cool air. The authors predict that as ambient temperature approaches body temperature, yawning should diminish, and when ambient temperature exceeds that of the body, yawning should stop. This might also explain why subjects with a warm compress applied to their forehead did not yawn more, since the body might detect the high temperature compress and interpret it as higher ambient temperature.

We are getting quite close to a Unified Theory of Yawning. Even though the physiology and neurology behind it is very complex, we seem to be moving in the right direction. We can even make some evolutionary hypotheses about yawning without sounding entirely speculative. For example, we might say that a population in which yawning is contagious will be more synchronised and better able to maintain its function as a unit, whether that involves moving around at specific times of day, making sure no-one wanders off after bedtime or keeping safe from enemies. Hopefully all the yawning you just did while reading this article was only because just thinking about it makes you yawn.


Andrew C. Gallup, Gordon G. Gallup Jr. (2007). Yawning as a Brain Cooling Mechanism: Nasal Breathing and Forehead Cooling Diminish the Incidence of Contagious Yawning Evolutionary Psychology, 5 (1), 92-101

Also, a website entirely dedicated to yawning called Baillement, which is French for "yawn". Lots of papers to read with some comments by the website authors themselves.

Monday, 11 June 2007

Cell death, is it all about apoptosis?

Where would you be without cell death, well dead I reckon. Cell death is needed in development to shape you body, such as give you fingers by killing the webbing between them. Not only that, but cell death is needed to shape the development of the brain. These things are done by apoptosis, what I would describe and the clean way of dealing with dead cells. They get broken down by nice signals outside the cell or if something internal goes wrong they order themselves to die (like by p53 to stop the cell becoming a cancerous cell and killing you). When they break down they do it in such an ordered way you wouldn’t really notice it, the dead parts get eaten up by near by cells and no nasty lysomal enzymes get released to damage the rest of the tissue. However not all cells die in this lovely way. Necrosis is where the cell is damaged and really just bursts open and releases lysomal enzymes that damage the tissue and it causes an inflammatory response by releasing HMGB1 from the nucleus into the extracellular environment to clear away the corpses of the cells.

However the two may not be so distinct. The same injury can cause either and if the apoptosis mediators are not functioning through mutations then necrosis can take over. If ATP levels drop in a cell going through apoptosis necrosis kindly steps in and does the job. Necrosis seems to have a controlled cellular pathway involving ROS, calcium signalling and proteases being activated. Some of the necrosis program appears to work in the background of apoptosis and parts of apoptosis keep the death ordered. Necrosis also (sometimes) is beneficial to an organism. In rabbits it has been reported that excess cells in theur growth plates down by necrosis.

So necrosis may be damaging and causes a lot of brain damage in strokes and Alzheimer's disease, but it is probably a backup program for when apoptosis fails to handle the situation rather than simply the cell bursting open!

The figure is from: Leist M. and Jäättelä M. (2001) Four deaths and a funeral: From caspases to alternative mechanisms. Nature Reviews Molecular Cell Biology 2: 1-10.

Saturday, 2 June 2007

Dosage compensation- not the textbook version

As usual (or as necessary) we were taught the textbook version of something... in this case dosage compensation. Yes, it is true that in mammals one of the X chromosomes is randomly inactivated to form a mass of heterochromatin known as a Barr body... but is this the end of the story?

Dosage compensation is a necessity in any organism with morphologically different sex chromosomes. If no compensation occurred, then the homogametic sex, e.g. XX females in humans, would show twice as much X-linked genes expression than males. It just happens that inactivation of one of the X chromosomes is only one of the possible strategies.

In Drosophila there will be a two-fold increase in X-linked expression in males. This is possible through a protein complex called MSL (male-specific lethal) which includes enzymes involved in acetylation and phosphorylation of specific histone amino acids (characteristic marks of active chromatin). The complex is targetted to the X chromosome through hundreds of binding sites with variable affinities for the complex.

C.elegans shows a strategy more similar to that of mammals. However, instead of inactivating completely one of the Xs, it will partially repress both Xs on hermaphrodites (XX). It also uses a protein complex, DCC (dosage compensation complex), but its characteristics are quite different from that of MSL- it includes no enzymes, and no non-coding RNAs. Due to its homology and shared components with the 13S condensin complex, responsible for chromatin compaction during meiosis and mitosis, DCC is thought to repress transcription by positively coiling DNA.

In mammals we already know what happens... However there is no primary protein complex- it is a non-coding RNA, Xist, that will spread from XIC,
a 1 Mb region in the X, and coat one of the X chromosomes. It will then allegedly recruit other proteins that mediate the epigenetic changes characteristic of the inactive Barr body. How the choice is made is not known, but a recent study suggests that the two XIC (one in each X chromosomes in females) can physically pair, which may be involved in determining which of the two is inactivated.

To finish off, and off course after reiterating that the story is even more complicated than that, it is important to say that even if we consider only mammals, not everything has been told to us. In fact, X inactivation does not always occur at random. It happens that in certain mammals, namely in mice, at the early embryo stages there is imprinted X inactivation of the paternal X only. This is, however, reverted in the cells of the inner cell mass, which will then undergo normal random inactivation... Of course we can't be told everything in lectures... but is interesting nevertheless to find these things out later on!
Two references:
Ng K., Pullirsch D., Leeb M., Wutz A. (2007). Xist and the order of silencing, EMBO Reports, 8. pp 34-49
Straub T., Becker P. (2007).Dosage compensation: the beginning and end of generalization, Nature Reviews Genetics, 8. pp 47-57