Epigenetics – Putting the “epi” in epic

The latest craze in the world of science is to talk about epigenetics. You may have heard about it on TV or read about it in the newspapers, quite probably associated with some wonder cure or a way of shaking off those pounds without having to do anything.

Epigenetics is an extremely young area of interest in biology. It differs from good old-fashioned genetics in that it does not concern itself with the DNA sequence. Instead, it deals specifically with how chemical modifications made to the DNA and/or the proteins with which it associates (histones) can affect gene expression. It is an area of great interest because this regulation can have quite dramatic consequences, despite being relatively short-lived. These chemical modifications can be made and unmade very quickly, and thus ‘kick-in’ rapidly, yet can be triggered by simple changes in factors such as diet or exercise.

DNA is a long chain of individual molecules called nucleotides, which have three main parts: a deoxyribose sugar, a phosphate group and a base. There are four possible bases, which may be found in DNA (G, A, T or C) and certain sequences of these bases are used to encode proteins.

DNA molecules are enormous in length, as you might imagine given that they encode a human being. [Insert dubious statistic about length of DNA and distance to the Moon & back]. This presents a logistical challenge, because this information has to be readily accessible so that it can be read and copied to make proteins, yet it must also be stored away and protected within the small space of a cell’s nucleus.

The way in which nature has achieved this is by developing protein molecules around which the DNA can wind – the histones. Long chains of DNA wound around histone complexes coil and wind up even further, ultimately giving rise to the familiar ‘X’-shaped chromosomes that are seen during cell division (Figure 1).

Figure 1. Zooming out from DNA (1), to DNA wrapped around histones (2), through to an entire X-shaped chromosome formed from lots of DNA wrapped around lots of histones (5). Image source: Wikimedia Commons (Author: Magnus Manske). Image used under Creative Commons License 3.0)

Figure 1. Zooming out from DNA (1), to DNA wrapped around histones (2), through to an entire X-shaped chromosome formed from lots of DNA wrapped around lots of histones (5). Image source: Wikimedia Commons (Author: Magnus Manske). Image used under Creative Commons License 3.0)

 Figure 2. DNA wrapped around a histone (Image source: Wikipedia (Author: PDBot). Image used under Creative Commons License 3.0)

Figure 2. DNA wrapped around a histone (Image source: Wikipedia (Author: PDBot). Image used under Creative Commons License 3.0)

The phosphate groups carried within the backbone of the DNA give it a strong negative charge. Figure 2 shows how the protein has many positively-charged ‘tails’ reaching out towards the coiled DNA. These opposite charges attract to keep the DNA tightly wound and stable. When the time comes that some of this DNA needs to be accessed to be read, there are enzymes that attach modifications (e.g. methyl groups –CH3) to the protein’s ‘tails’ to remove their positive charges. These modifications are completely reversible and provide flexibility in regulating which genes can be activated at a given time.

Methyl group modifications can also be attached to the bases within the DNA. This is yet another element of epigenetics and it works in a similar way to histone modification. These groups recruit proteins that block the DNA-reading machinery from accessing the DNA.

Why is this important?

This system adds a sophisticated level of control to gene expression and regulation. This is part of what allows us, as multicellular organisms, to exist. Breakdown of this control can lead to disease and has been shown to have an important role in cancer. Harnessing the power of the ‘epigenome’ is of intense medical interest for the development of new drugs and in the use of stem cells.

The importance of epigenetics is emblemised by the field of stem cell research. In the stem cells of the embryo all genes are accessible and there is very little epigenetic control. This is important because these cells will go on to differentiate and form all of the many varieties of cells in the body. Such stem cells, with the ability to become different cell types, are said to be ‘pluripotent’.  But, as these stem cells differentiate and become more specialised towards a particular task, the level of epigenetic control tightens, effectively closing off whole portions of the genome that are irrelevant for a particular cell type.

In 2012 Sir John Gurdon and Shinya Yamanaka won the Nobel Prize in Physiology and Medicine for their “discovery that mature cells can be reprogrammed to become pluripotent”. They found that the introduction of just four different proteins that help regulate gene expression (transcription factors) is sufficient for the reprogramming of a mature cell into a pluripotent stem cell. These transcription factors serve to wipe the epigenetic slate clean, and actually erase modifications at the epigenetic level to reopen the genome.

These cells can differentiate into any other cell type, meaning that it might, one day, be possible to generate replacement cells and tissues might to treat a huge range of medical conditions including heart disease and Alzheimer’s Disease.

This post, by author James Torpey, was kindly donated by the Scouse Science Alliance and the original text can be found here.


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Chocolate: the science of sweet

image1Rich, sweet and creamy with a sensuous ‘melt in the mouth’ texture. Chocolate is a guilty pleasure many of us share and, with Easter just around the corner, indulgence seems mandatory. But, what effect is our sweet tooth really having on our bodies and is there any scientific merit to claims that chocolate is actually good for us?

The medicinal use of chocolate has a long and rich history, with travel accounts and medical texts (dating from the 16th century) documenting a myriad of uses in the treatment of human disorders. These treatments range from the downright bizarre, to the infinitely plausible. For example:

Francisco Hernández (1577) wrote that pure cacao paste prepared as a beverage treated fever and liver disease. He also mentioned that toasted, ground cacao beans mixed with resin were effective against dysentery and that chocolate beverages were commonly prescribed to thin patients in order for them to gain “flesh.” William Hughes (1672) reported that coughs could be treated by drinking chocolate blended with cinnamon or nutmeg. While De Quélus (1718) wrote that drinking chocolate was nourishing and essential to good health. He said that drinking chocolate “repaired exhausted spirits,” preserved health, and prolonged the lives of old men. – For a more detailed overview of chocolate’s rich history, see here.

But do any of these claims hold water in the face of scientific scrutiny?

Chocolate: a way to the heart.

Dark chocolate and other cocoa products have, on a number of occasions, made the headlines as a dietary supplement and means to decrease blood pressure and modify other cardiovascular disease (CVD) risk factors (see here and here).

image2This line of research stemmed from observations among the Kuna Indian population in the san Blas Islands of Panama. Members of this population were seen to have particularly low rates of hypertension and CVD, coupled with an absence of age-related increases in blood pressure. Scientists theorised that theses unique medical traits were linked to high levels of cocoa intake amongst this group – On average Kuna Indians consume four 8-ounce cups of unprocessed cocoa drink per day!

One explanation for these findings is cocoa’s high flavanol content – which is thought to confer cardiovascular benefits through its effects on the circulatory system. Indeed, flavanol-rich cocoa may improve functionality of the bodies blood and lymph vessels and reduce various factors which may otherwise increase an individuals risk of CVD.

Alongside flavanols cocoa also contains an organic alkaloid compound called theobromine. The effects theobromine has on the body are pretty similar to those of caffeine, only slower to take effect – so perhaps a hot chocolate before bed time may not be a great idea. Alongside its caffeine-like properties, theobromine also acts as a cough suppressant, many ease the symptoms of asthma and, like flavinols, could improve cardiovascular health.

But, chocoholics beware, these findings do not prove that gorging on the brown stuff is actually good for our health. Firstly, the flavanol content of chocolate varies hugely depending on how the chocolate is processed. In fact, since flavanols are naturally bitter, these are usually thought of as unpalatable in the west and are generally reduced during the processing of our favourite chocolate treats. The cocoa powder consumed by the Kuna indians contains about 3.6% flavanols, while western chocolates range in their flavanol content – the highest being found in dark chocolate at 0.5%, while milk and white chocolate can sometimes be completely flavanol free. This means that, in commercially available chocolate products, the health benefits of flavanol are largely removed by the manufacturing process.

It’s also important to remember that most commercially available chocolate has a high caloric content and contains a significant amount of saturated fat and sugar. We know that excessive caloric intake can lead to some pretty adverse metabolic side effects (weight gain, diabetes perhaps even alzheimer’s disease) which probably negate any health benefits. This means that doctors would generally err against recommending chocolate as part of a healthy diet, with the possible exception of high quality dark chocolate.

So when it comes to a healthy body, the science of chocolate is not exactly black and white (or dark and milk) but, what about the effect it can have on the mind?

Chocolate on the brain:

in 1718 De Quélus wrote that chocolate can “repair exhausted spirits” and many people claim that indulging in the brown stuff can indeed be the perfect cure for low mood. But, how does chocolate effect the brain and, is the hedonistic pleasure of a good binge physical or psychological?

Chocolate consumption has been linked with a number of neurotransmitter systems, which play an active role in appetite, reward and mood regulation (including dopamine, serotonin and endorphins). However, there is currently insufficient evidence that these effects are specific to chocolate, or that they have an overall positive effect on mood.

340234_10100270433865775_1275067435_oInterestingly, although chocolate and junk food are regularly cited as the ‘go-to’ home remedy for malaise, extensive studies fail to find any real or lasting benefits to these binges. In fact, the opposite may be true, as often the guilt associated with a binge can leave sufferers feeling much worse!

So sadly, although a nice chunk of chocolate may provide brief pleasure and comfort, in the long term it’s more likely to prolong rather than abort a low mood.

So, chocolate is a mixed blessing. There’s almost certainly no harm in the occasional indulgence and, when it comes to high cocoa content dark chocolate it could even be beneficial. But, when it comes to our health, chocolate should definitely be considered a treat and not a lifestyle. That said, it won’t stop me enjoying my easter eggs this year!

Post by: Sarah fox

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Breaking Brain: Computer Science of the future

image1Code breaking all sounds very ‘007’ (or a bit Alan Turing if you’re into your WWII and Manchester history). For many it conjures images of special agents embroiled in top secret espionage; or perhaps a lone revolutionary working by candlelight towards some crucial eureka moment. But, what about breaking the ultimate code, that of the brain? Here I’ll explore some real life advances in neuroscience which may sound like science fiction, but are, in fact, all real…

Communicating with vegetative patients using neuroimaging:

No, this isn’t a work of science fiction; using state of the art technology, outwardly unresponsive patients can now communicate with the outside world (see here for the full article)

Due to developments in neuroscientific research, we can predict what brain activity will look like when people are asked to imagine performing certain actions (such as playing tennis); and, amazingly, it is this knowledge that forms the basis of such communication.

image2Scientists asked outwardly unresponsive patients yes or no questions whilst scanning their brains using functional magnetic resonance imaging (or fMRI). Patients were instructed to imagine playing tennis if the answer was yes, or to do nothing if the answer was no. Incredibly, it was found that one patient who had been outwardly unresponsive for five months following a road traffic accident, was able to respond in this way. Scientists could be sure that this was a specific response to their question (and not just random brain activity) because of the well-known brain ‘signature’ which follows the imagination of playing tennis. Indeed the patient’s brain responses for this task could not be distinguished from those of a normally functioning person performing this task. Technology such as this could help physicians to make crucial decisions about the care of outwardly unresponsive patients, and could help families find ways to communicate with their loved ones.

A window on the mind:

Some neuroscientific research can ‘train’ computers to respond or learn like a human brain – so called ‘neural network models’. One notable example of this is the work of Nishimoto and colleagues from Berkeley, USA. Nishimoto and colleagues used fMRI to scan the occipital cortex (the visual centre in the brain) of people watching clips of movies. The movie scenes were then categorised mathematically on a great number of features (e.g. the presence of colour, the nature of any movement, the presence of lines etc.). With this data, scientists set about developing a model that could match the mathematical categorisation of video data to real-time brain activity. Essentially, this involved looking for patterns in the mathematical categorisation that matched patterns in brain activity; such that one could say when a person views a picture with property A, then brain activity pattern B is reliably produced. The more movie clips and brain activity that were analysed, the better the model became.

image3Incredibly, the finished model could take fMRI data from an unknown clip and generate an accurate visual representation of the associated movie. Take a look at the YouTube clip that shows this happening here, and/or read the full scientific article here.

If you’re not already excited by this, just imagine the possibilities with a tool like this… Ever wanted to remember your dream from the night before but it all seems a bit vague and out of reach? It’s theoretically possible that this technology could ‘record’ a dreamer’s visions. And, what about recording your thoughts and even feelings for future playback?

Although this is beginning to descend into ‘science-fiction’; the basic premise of using computer science to model human behaviour could in theory, be applied to any modality from vision to touch – and who knows, maybe one day, feelings and emotions. With the ever growing and impressive repertoire of neuroscientific advances, it seems that today’s musings could be tomorrow’s reality.

Post by: Gemma Barnacle



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Don’t be left in the dark: eclipse facts.

A solar eclipse is one of the few astronomical events that actually gets people on mass to look up and think about what happens in the heavens. In this article, I want to indulge your astronomical interests with five interesting eclipse facts alongside a few of my own images of todays eclipse.

1. We can all agree that an eclipse is a pretty rare event, but you may not know that todays eclipse is especially unusual! This is because it occurred on the spring equinox and also reached the North Pole. This is the first time the North Pole has seen the sun for over 6 months; meaning that anyone, or anything, up at the Pole would have had to endure an extra few minutes of darkness because of the eclipse.

2. The movements of celestial objects are amazingly regular and cycles of movement can be predicted long in advance. Solar eclipses, like the one we saw today, are the result of ongoing cycles which repeat every 18 years, these are called Saros cycles. Many Saros cycles run simultaneously and todays eclipse was part of cycle #120. That means that, although the next eclipse in cycle #120 will not occur for another 18 years, similar eclipses will occur as part of other cycles. Therefore, there will be another total eclipse next year, this will be part of another Saros cycle (#130) and will be visible over Indonesia and the Pacific ocean. These cycles do not continue repeating forever actually, after about 1300 years, each Saros cycle stops, and a new one takes its place. Sadly, despite the wealth of Saros cycles running right now, we wont actually see another total eclipse in the UK until 2090.

3. Solar eclipses occur because of an amazing coincidence. The Sun is about 400 times larger than the Moon but the Moon is about 400 times closer. Therefore both appear to have the same size in the sky (about 0.5 degrees of arc, which is approximately the size your thumb when you extend your arm). – As explained perfectly here by Father Ted Crilly.

4. Eventually we will no longer witness any Solar eclipses. This is because the Moon is slowly moving away from the Earth; but why? The Moon exerts a gravitational force on the Earth that ‘deforms’ the oceans. We notice this affect in the form of tides. Over time, this deformation of the oceans exerts a small gravitational force back on the Moon which accelerates it, pushing it away from the Earth whilst also slowing down the Earth’s rotation. Eventually the Moon will be too far from the Earth to fully cover the face of the Sun and the solar eclipse will become history.

5. Solar eclipses allowed physicists to test general relativity. When light travels close to a massive object (such as a galaxy) its huge gravity actually bends the light slightly towards it. When you calculate this bending affect, using old Newtonian physics and newer general relativity, you get different answers. What was needed was a test. In 1919, Sir Arthur Eddington found that if you could measure the position of a star whose light past near the Sun then you could calculate the true light bending affect of the Sun’s gravity. He could only perform this measurement during a solar eclipse because most of the Sun’s glare is blocked out by the passing Moon, meaning that he could observe stars appearing near the Sun. He found that their positions, relative to other night sky objects, changed very slightly when they were influenced by the Sun’s light-bending gravity. Indeed, the amount of bending was found to agree with…you guessed it…general relativity.


Today’s eclipse viewed from Bury Lancashire.

Guest post by: Dr. Daniel Elijah

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A brief history of getting your groove on:

6975100728_d9edb36f91_zWhether you’re a fan of classical quartets or acid house, one thing is certain; we all love a good tune! Music has the amazing ability to drive our emotions, bring people together and encourage us to dance till dawn. But why should this be the case? It’s easy to understand how pleasure can be derived from food and sex and why bereavement makes us sad. But, what is so special about music? The ability to write a good tune has no evolutionary advantage….or does it?

Novel research from our own fair city (Manchester) is now combining evolutionary biology, physics and neuroscience in an attempt to uncover the mysteries of music and its effect on the brain. This work, led by academic and musician Dr. Neil Todd, has uncovered a biological pathway linking sound, movement and pleasure in the brain. This pathway may have remained elusive for so many years because of its unusual origins. Neil has found evidence that, contrary to the traditional textbook theories, the cochlea is not the only sensory organ in the inner ear capable of responding to sound. His research suggests that the vestibular apparatus, normally associated with balance and spatial orientation, is also sensitive to certain frequencies of sound.

ROSERENASSThis may seem like a kooky idea but, viewed from an evolutionary standpoint, it actually makes perfect sense. In mammalian anatomy, we know that the cochlea is responsible for perception of sound. But, looking back down the evolutionary scale we find that this organ is not always present. Taking bony fish as an example, we find no sign of a cochlea. But, fish are far from deaf; in fact they use their otolith organs (part of the vestibular system) to detect vibrations. Similar to the human cochlea, the fish otolith organ contains an array of tiny hair-cells which can detect vibrations and translate these into a sensation of sound. Alongside fish, there are also many further examples of creatures utilising their vestibular sensors as sound detectors. So, there’s certainly evolutionary precedence for a mammalian vestibular sound processor. But, can humans use this system to perceive sound and, if so, why might this be advantageous?

Using electrodes which measured electrical signals from the neck and eyes (specifically from muscles responsive to vestibular activation). Neil found that the human vestibular system was sensitive to air-conducted sound frequencies ranging from 50-1000Hz, peaking between 300 and 350Hz – just above middle C on a musical scale and a similar frequency to male and female voices. For head vibration the peak sensitivity is even lower, at around 100 Hz. Taking this work one step further, Neil’s group wired up a number of participants looking at electrical activity in the brain and vestibular activated neck/eye muscles simultaneously. This method enabled the group to discern how responses in the brain differed between sounds which activated the vestibular system and those which didn’t. It was discovered that sounds falling within vestibular-activating frequency bands caused activity in auditory cortex and cingulate limbic areas, as well as sub-cortical areas traditionally associated with vestibular activation. This strongly suggests that certain sounds can indeed activate the human vestibular system, but why might this be useful?

Once again peering back through our evolutionary past, we find that many creatures use vestibular-activating sounds as mating signals. Have you ever heard a fish sing? Well, he may not get a turn from the judges on ‘the Voice’, but the male Haddock is one of the most vocal of fish and he uses his alluring voice to snag himself a mate. Male haddock vocalise by drumming on their swim bladder and, if surrounding females, are charmed by this song the music can cause both fish to simultaneously release eggs and sperm. Again, it seems that many creatures use this sense when finding a mate, and many also accompany this behaviour with a kind of dance. Therefore, it is possible that the vestibular sound-sensing system represents an ancient pathway used in mating behaviour – perhaps similar to the recently discovered vomeronasal system used to choose a mate based on pheromones and smell.

6307084759_7527ac5fef_zSo, perhaps our love of music and the intoxicating atmosphere of nightclubs could be the upshot of an ancient evolutionary system linked with fundamental mating behaviour.

Post by: Sarah Fox

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Are all owls really nocturnal? : And other common misconceptions about owls

We’ve all been brought up (particularly in the UK) with common myths about owls; they all say ‘twit twoo’, they can turn their heads all the way round, they’re all nocturnal and of course that they are the wisest of all creatures. But how many of these are actually true?

If you ask any child or even an adult what sound an owl makes they will answer with ‘twit twoo’, and how they sometimes hear the noise of the owl down a quiet dark country lane at night. Firstly, the only owl that says ‘twit twoo’ is the tawny owl, Strix aluco, and it’s actually a breeding pair, the male emitting the ‘twit’ and the female the ‘twoo’ sound. However, the tawny owl, one of five recognised and protected British owl species (along with the barn owl, the little owl, the long eared owl and the short eared owl) is the most common of all the owl species in this country, so the chances of you hearing the ‘twit twoo’ sound is much more likely than hearing the screech of the barn owl for example.

How about the myth that they can turn their heads all the way around, or as a little girl once told me ‘they can turn their heads around and around and around…’? I’m afraid the truth is if this was the case the owl would choke or its head would fall off! However, owls can turn their heads up to 270 degrees each way (left or right) and 180 degrees upwards, and they do this by having twice as many vertebrae in their neck than mammals do. But why do they do this? Having such large eyes means that their eye sockets are fixed in their skull, so unlike us they can’t look left or right by just moving their eyes. Instead owls have to move their whole head to focus their eyes on their prey.

Next, the common thought that all owls are nocturnal. Again a myth I’m afraid. Although about 60% of all owl species are nocturnal, the rest are diurnal (active during the day) or crepuscular (active at dawn and dusk). Interestingly, you can actually figure out when each species of owl is most active by simply looking at their eyes. If they have black eyes they’re nocturnal, if they have yellow eyes they’re diurnal and if they have orange eyes they are a crepuscular species (see figure 1). Pretty neat, right?

Screen Shot 2015-03-08 at 14.16.13

Figure 1: A) snowy owl (Bubo scandiacus) with yellow eyes is a diurnal species, B) European eagle owl (Bubo bubo) with orange eyes is a crepuscular species and B)Tawny owl (Strix aluco) with black eyes is a nocturnal species

Finally, the myth of the wise old owl has existed for thousands of years, ever since people worshipped the Greek goddess of wisdom, Athena, who had a pet owl (see figure 2). Clearly people assumed that if Athena was wise, owls must be too. This myth has continued into modern culture with characters such as ‘Owl’ in Winnie the Pooh and ‘Archimedes’ the owl in The Sword in the Stone (great film though :D). The truth is owls are clever when it comes to hunting, but really that’s all they need to be able to do. They don’t need to figure out the answers to a crossword puzzle like we might try to do, or decipher the instructions to microwave a meal, they need to hunt and they’re very good at it. The reason for the case that owls are not ‘wise’ is because underneath all the fluff and feathers they have a skull the size of a golf ball and inside a brain about the size of a 5p coin; one third is used for eyesight, one third for hearing and one third for general thinking. So, although most of what you thought you knew about owls may not actually be true, I’m sure you agree they are still incredibly fascinating creatures.


Figure 2: The owl of Athena

This post, by author Alice Maher, was kindly donated by the Scouse Science Alliance and the original text can be found here.

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The X-Club

Upon first hearing of ‘The X-Club’ you probably imagine a group of superhumans, responsible for saving the free world from some terrible intergalactic catastrophe. However, they were in reality a group of Victorian scientists that were instead responsible for saving the UK from scientific ambivalence, arguably the more impressive of the two feats.

The Original X-Club

The Original X-Club

Among The X-Club’s nine members were the brilliant biologist T.H. Huxley, the prodigious physicist John Tyndall, and the spectacular sociologist Herbert Spencer. All of the members were driven by a conscious decision to rail against the traditions of the church-driven scientific agenda, claiming cultural leadership for the scientists of the day. As well as campaigning vigorously for the evolutionary theories of Charles Darwin (more of which here), they also solicited government support for science, procured jobs for scientists and were instrumental in demanding that science be taught at every educational level.

As well as being brilliant scientists in their own right, these Victorian gentlemen were also outstanding communicators, utilising a variety of media to explain science to a range of different audiences. Amongst other activities, they wrote textbooks, contributed to scientific journals, gave popular lectures and advised politicians. In short, they were science communicators extraordinaire, laying the foundations for the relatively egalitarian environment in which we as scientists now operate. Superhumans they may not have been, but that only serves to make what they achieved all the more remarkable.

The original X-Club had a total of nine members, who were active from 1864 to 1892. In the spirit of this original troupe I now offer the following members for consideration into ‘The XX-Club’, so called because they now welcome into their ranks three female members:

Professor Brian Cox AKA ‘The Dream’

Sir Tim Berners-Lee AKA ‘The Web’

Professor Nancy Rothwell AKA ‘The Balance’

Professor Richard Dawkins AKA ‘The Watchmaker’

Baron Robert Winston AKA ‘The Body’

Dame (Susan) Jocelyn Bell Burnell AKA ‘The Pulse’

Sir David Attenborough AKA ‘The Silver Back’

Baroness Susan Adele Greenfield AKA ‘The Brain’

Professor Stephen Hawking AKA ‘The Fourth Dimension’

My only criteria for selection were that these were scientists who were well known for both their research and also the promotion of their field to the general public. In keeping with the original X-Club, I also limited my selection to those scientists currently working in the UK.

Looking at this selection it is interesting to see that it is fairly dominated by physicists, with a third of the members conducting research primarily in that area. Whilst I admit that part of this might be to do with my own background (MPhys in Physics with Space Science and Technology, PhD in Atmospheric Physics), I also think that it reflects the zeitgeist of the current popularisation of science. Just as the dominance of the original X-Club by evolutionary biologists (three of the nine members were practitioners of either Natural History or Natural Philosophy) reflected the prevalence of Darwinism in the psyche of the public consciousness, so too does the make-up of The XX-Club mirror today’s fascination with the exploration of the very large (via space exploration) and the very small (via particle colliders). Whether or not that is a case of cause or effect is a debate for another day. For now, let’s just marvel at the quality of the current crop of science communicators that make such a debate possible.

Post by: Sam Illingworth

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