December 16, 2013
On the origins of sexuality

Homosexuality is a divisive, controversial topic. The controversy isn’t just confined to homosexuality of course, the same problems go for bisexuality, asexuality and transgender. Science and reason are prime vehicles for progress and it is through these I address controversial debates.


It is important to treat such issues with maturity

The most clear evidence suggesting a natural role for homosexuality is it’s existence across the animal kingdom. The earliest documented cases of animal homosexuality date back 2,300 years to the work of Aristotle. Up until now homosexual behaviours have been observed and documented in penguins, bats, seals, rats, walruses, sheep and chimpanzees, amongst other animals I can’t recall right now.

Research conducted in fruit flies by Grosjean et al in 2008 showed that specifically altering neuronal biochemistry (in particular, glutamate signalling) could render males ‘gender blind’. The resultant chemical change caused broadly bi-sexual behaviour to occur in male fruit flies. Of course, it is very important to note that expressing the same change in human brains would not have the exact same effects as happened in the fruit flies. Our brains contain greater complexity, it would seem. The principle the fruit fly study highlighted is the chemical nature of sexuality, based on interfering with basic neurochemicals and genes which are present in both flies and humans, and used for largely similar tasks.

Sheep are a prime animal model when studying sexuality. Rams have been characterised to naturally exhibit 4 sexualities; heterosexual, homosexual, asexual and bisexual. Males are generally studied as they are the active initiators of sexual interactions in sheep. Numerous studies have been conducted into this occurrence, suggesting that 8% of rams in a given population are ‘male oriented’, meaning they prefer to mount males instead of females.


Fus Roh Dah!

Understanding of how sexual behaviour is programmed into the mammalian brain has been unraveled through studies into rodents and rams. The earliest studies go as far back as the 1950’s where Phoenix et al demonstrated the presence of testosterone in guinea pigs could masculinise and defeminise the developing female brain. This study is not unique and more recent follow up studies in rats have since confirmed this. It is suggested there is a critical period in early development where hormonal feedback from the developing gonads ‘set’ the brain on its eventual course to sexual identity, which (from an evolutionary standpoint) should enable the organism to select a mate and continue the species. A study into female rats conducted 2011 (Henley et al, 2011, Hormones and Behaviour) showed that treatment of the developing rat brain with the oestrogen, oestradiol, influenced female rats to ignore sexually active males and spend time with other female rats, particularly those on oestrus.

The science underlying the hormonal effect on sexual preference explains that the developing testes release testosterone into circulation and back to the brain, resulting in the development of a male brain. The absence of testes, via the absence of the Y chromosome, would allow foetal development in the default female state. Altering this hormonal state could affect how the brain responds to hormonal cues. Elevating oestrogens in a male brain may influence some parts of it to feminise.

Studies in humans have shown differences in brain structure between hetero and homosexual males. Most notably in a region of the hypothalamus called the Suprachiasmatic Nucleus (SCN). This region is principally implicated in the body clock. This particular anatomical difference may simply be a consequence of another underlying process and not really anything to do with body clock function. A study by Swaab et al in 1995 showed an increased SCN volume in homosexual men (via post mortem examination of men who died from AIDS, it was concluded that AIDS did not affect SCN size). The study showed possible metabolic differences in the hypothalamus between homo and heterosexual men, though the study did not elaborate on why this occurred. Further studies by Swaab and colleagues induced this change in SCN size in rats, which subsequently grew up to exhibit bisexual behaviours. The results aren’t identical as the rats mated with females as well as males, but the important thing to note here is that male preference was generated in these rats (and there is the species difference to account for, too). The interesting aspect of this study was how they replicated the increased SCN size in the rats. This was achieved via interfering with developmental brain sex-hormone levels.


location of the SCN

In line with the aforementioned experiments on rats and rams, the prevailing hypothesis for formation of sexual preference in humans is that the sexual anatomy of the brain is likely influenced by the levels of sex hormones (testosterones and oestrogens) in the womb. We’re all mammals after all and share a common developmental biology. These hormone levels may fluctuate due to natural biological variation, the environment the mother is exposed to and a whole host of other factors. With homosexual males and females, the full development of a sexually different brain is likely NOT occurring. What appears to be happening is the masculinisation and feminisation of particular regions of the brain, so the person may retain other gender typical traits, but merely have a difference in preference. In humans, this is difficult to test fully at this stage.

 To throw another spanner in the works, the process is not completely straightforward as further sexual development occurs during puberty. It may be the case that the sexual development in the womb may predispose a certain sexual preference, but perhaps environmental and psychological input into the developing adolescent brain may also steer where the sexual preference ultimately rests. Finally, there is the inference that due to varying levels of sex hormones influencing brain development in the womb, sexuality may lie on a continuum. It may not just be strict categories of hetero – homo – bi etc. It may well be a gradient, or an assortment of sexual behaviours, dependent on developmental circumstance.

Atypical sexual preference may not simply be a persistent evolutionary accident (though it may have started out as one); such behaviours have been suggested to have useful social roles in social organisms.

 A lot more study needs to be done to provide more conclusive evidence in humans, but the results so far are promising. The wealth of findings from numerous laboratories from across the world are in conflict with old fashioned schools of thought that the atypical sexualities are unnatural, immoral choices. Perhaps it is time information on the science is disseminated more widely. I can see why such information isn’t widely distributed as it can be difficult to digest. Furthermore, the fabled ‘silver bullet’ hasn’t arrived for the science of sexuality, perhaps putting it low on the radar of news-science reporting. But science doesn’t always wait for a magic study which suddenly validates a field. It is often a long, arduous accumulation of evidence, peppered with criticism and reason, but ultimately relies on a consensus. Some science does get that single defining study, but at this point the science of sexuality is left wonting.


December 13, 2013
Life on the radiowaves


Our sun is a ball of hydrogen. The hydrogen atoms constituting the sun are subject to immense physical pressures, causing them to fuse with each other to create heavier elements. In addition to creating heavier elements which could potentially create planets at some point in the distant future after the sun dies, this process of nuclear fusion releases a lot of energy. This energy is released in the form of waves. Photons are particles which denote packages of energy, and they can travel as waves (bizarre). These are radiated in all directions and the Earth is in the path of this barrage of solar radiation.

The type of radiation emitted largely depends on the energy of the photon or wave being emitted from the fusion event. Let us bear in mind that the sun is incredibly large and hydrogen atoms are the smallest of the elements, so there are A LOT of hydrogen atoms to fuse. Half a gram of hydrogen can generate 500 megawatts of power, via nuclear fusion. The sun fuses about 500 million tonnes of hydrogen every second. And it could keep doing this for a few billion more years. So that’s a lot of energy being released from lots of tiny atoms. Different photons being released carry different energies and this determines their properties as radiation, as they’re thrown out or ‘radiated’ from the sun.


The electromagnetic spectrum; waves of radiation

Low energy rays have long wavelengths and are largely harmless to most life. These include radiowaves. High energy waves have short wavelengths and high frequencies, and this energy allows them to interact with molecules and cause reactions between them. These can be dangerous to life as they can damage proteins and DNA. (Recall: living organisms are just complex, ordered systems of chemicals. We are subject to the same laws as the rest of matter).

One of the key events allowing complex life to evolve was the development of the ozone layer. This was only possible due to the release of oxygen from early organisms which released oxygen as a waste product from metabolism. Oxygen high up in the atmosphere reacts with the highest energy radiation, using up the energy in high energy free-radical reactions. This blocks out much of the most harmful radiation, including high energy Ultra violet, x-rays and gamma rays. Some do make it to the surface, but it’s not generally at high enough intensities.

A key mechanism underlying the interaction of radiation with matter involves electrons. As you may know, atoms are made up of subatomic particles, electrons being but one of these. Atoms are made up of a nucleus, which is orbited by electrons (-depending on ionisation, if you want to bring up electron-less hydrogen ions, but to the less chemically minded, don’t worry about this for now).


diagram of a basic model of the atom

Electrons form the bonds between atoms to create molecules. Recall, photons are a packet of energy. When they strike an electron, the electron gains this energy. Altering the energy of an electron can change its behaviour in a molecule or atom. Imbue it with enough energy and it may zip off from the atom, leaving it entirely. This leaves a weird electron deficient atom/molecule which wants to regain its electron to get back to its stable state so it may end up forming bonds with a neighbouring molecule. In complex biological systems, this can be highly disruptive. It can cause cross linking of nucleic acids in DNA, giving rise to mutations, or causing cell death. So you can see high energy radiation isn’t in the interests of our cells (though it can have uses in other applications, if controlled properly). In this way, scientific and medical equipment can be sterilised by subjecting it to high intensity high energy radiation.



Plants lead the way in making the most of radiation. Choloroplasts are tiny organelles within cells which contain the green pigments which harness the energy from visible and sometime ultraviolet radiation from the sun. The energy is used to transport electrons up a chain of electron acceptors to eventually assist in the production of the principle energy currency in living organisms on Earth, ATP. This can be used to power biological processes. Through this, plants and similar organisms (algae and cyanobacteria, amongst others) capture energy from the sun to form the basis of most food chains on Earth.


One type of this radiation which isn’t filtered out by the ozone layer is used by a great many organisms. Organisms use it to help them to sense their environment. This is known as the visible spectrum. Visible light consists of different sub frequencies which make up the different ‘colours’ as we perceive them. Light reflects off much of our surroundings, so being able to ‘read’ this light would inform us of the nature of our surroundings. Colours are merely evolution’s answer to interpreting different wavelengths of the abundant and usually safe visible radiation to give us (and other colour seers) more information about our surroundings.This process of converting radiation to vision works via the eye (surprise!). The retina is a structure at the back of the eye with specialised cells (rods and cones) which contain a pigment which responds to the radiation of a particular wavelength. Light strikes the pigment molecule, exciting the electrons enough to cause the molecule to change shape. This altered molecule goes on to effect proteins in the cell which transduce a nervous signal from receptor cell to be relayed back to the brain. Millions of these receptors responding to light sending simultaneous signals, are interpreted by the brain as an image.



The melanins are a class of compounds synthesised by cells from a diverse range of organisms. The primary goal of producing melanins is to absorb harmful radiation and shield sensitive proteins and nucleic acids from damage. In humans, we notice them in our skin (the pigment largely responsible for skin colour, or lack thereof) and in our irises.


Some organisms have adapted melanins to mimic the electron transport chain from chloroplasts in plants. Instead of responding to radiation in the visible and ultraviolet wavelengths, they can respond to anything up to gamma radiation. Organisms which feed off harmful radiation! Varieties of Cladosporium and Cryptococcus have been found thriving in the Chernobyl ruins, feeding off gamma radiation.

Vitamin D and the Immune system


The energy from radiation in the mid to lower Ultraviolet wavelengths is important in the synthesis of pre-vitamin D from it’s cholesterol-derivative precursor. Vitamin D is important in synthesis of bones and regulation of the immune system. Indeed, lack of UV exposure has been linked to increased incidences of multiple sclerosis in the Northern Hemisphere. Multiple sclerosis occurs when the immune system begins attacking myelin producing cells in the nervous system. It is hypothesised that lack of vitamin D reduces suppressive effects on wayward immune cells.


And finally, the obvious one. Not quite as important for warm blooded animals like us, but for reptiles like snakes and lizards the heat from the sun provides their bodies with the energy required to allow their metabolism to operate at maximal capacity. Heat from the sun principally reaches the Earth in the form of Infrared radiation, a lower energy waveform than visible light.


There’s probably more that I’ve forgotten to mention, but for now this will suffice. Our relationship with the suns’ radiation keeps us alive, from powering the food chain through plants, being a readily available source of information about our environment and just keeping the planet warm. Sure, radiation CAN be harmful. Don’t want prolonged exposure to high energy ultraviolet rays, and we have the Ozone layer to protect us from deadly ionising gamma and x-radiation. But it’s not all bad, so raise your Rad-X to the joys of radiation!



August 3, 2013
Sensible chemistry

Before we can actually perceive something from our environment. we need to be able to sense it. Sensation doesn’t necessarily always translate into perception within the mind. This translation from sensation to perception depends on the context of the sensation. The context of a particular sensation may be our emotional state at the time, our memories associated with the sense, our health status, what occurs as a consequence of the sensation amongst other things, or what happens to occur while we’re sensing that particular sensation. It is this context which influences how we perceive various sensations. 

Each sense is mediated through its own receptor and specialist organ. It is at this point that the external stimulus is transduced into something which can be encoded into electrochemical signals along our neuronal cells which then relay to the brain where they are interpreted to allow the body to respond, and potentially become consciously appreciated so a behaviour, memory, emotion or thought may be generated in response. Our senses provide us with the raw material with which we construct our reality.

For Vision , our eyes detect electromagnetic radiation, To hear, structures deep within our ears detect vibrations in the air around us, touch is the sensation of physical movements and pressure on our skin, smell (olfaction) interprets airborne chemicals and taste detects soluble chemicals in objects we are interested in ingesting.


Taste and smell are referred to as the chemical senses as they respond to specific molecules. As we all know, Taste is detected through taste buds on the tongue. Taste buds are housed within papillae. The 5 basic tastes are Sweet, sour, salt, bitter and umami. Each of these tastes is detected by a different type of taste bud, expressing different cell surface receptors on its taste receptor cells. These 5 different tastes are important in their own right, as they signal to the brain what the content of the food is, and this enables us to make a decision as to whether or not something is worth eating. 

  • Sweet tastes are generated from the presence of sugars, sucrose, glucose.
  • Sour tastes are generated from the presence of acid (chemically, the hydrogen ion).
  • Salty tastes arise from sodium.
  • The bitter taste is a response to toxins. Hence why we don’t much like bitter.
  • And umami is the taste of amino acids, such as glutamate. Important for sensing protein content.

There is some evidence to suggest that there may even be tastes designated for ‘metallic’ and ‘fatty’ taste, though this is not as yet conclusively proven.


The structure of tastebuds. Picture adapted from ‘The Receptors and Cells for Mammalian Taste’ by Chandrashekar et al, 2006, Nature.

Taste is sensed at the tongue and this is transmitted to the brain via the glossopharyngeal and facial nerves, These nerves enter the brain at the brain stem where the information is transmitted to various regions of the cortex. The integration and processing of sensory input from the tongue mainly occurs in the gustatory cortex, which is housed around the Insula and frontal operculum region of the temporal lobe. (The processing of gustatory stimuli may not be exclusive to the gustatory cortex, there may be a more diffuse component to it). The somatosensory cortex will interpret tactile information. This is important concerning the texture of the food, and will integrate with information from other sensory modalities to construct a final percept of the food. The gustatory cortex then projects information to the limbic system and the orbitofrontal cortex. The limbic system will be involved in the emotional and memory aspect of the processing of the taste, helping to generate a preference or aversion to the food, based on previous experiences, or social context. The orbitofrontal cortex may play a role in conscious appreciation of the food.


The gustatory pathway

The innate responses to umami and sweet are generally positive, there is an innate ‘good taste’ associated with foods which come across as sweet or umami. The evolutionary reason being sugars are an immediate and useful energy source. Umami, indicating amino acids (the building blocks of proteins), signals protein content - also vital biomolecules.

Bitter and sour have innate aversive responses. Bitter taste is a response to toxins in food. We have evolved to recognise certain classes of compounds as potentially hazardous. Sour is aversive because the internal environment of the body must strike a delicate pH balance. Adding acid to this could potentially damage the digestive system, or indeed alter the pH of the blood, leading to disruptions in homeostasis.

Salt is an interesting one. Our ability to taste salt is an important regulatory mechanism for the body to control its salt levels. Salt is vital for neuronal function, amongst other functions in the digestive system and basic cellular homeostasis. So too little salt isn’t good, but too much salt would also cause many problems. Acceptable levels of salt appear to interact with a specific salt sensing receptor, called the epithelial sodium channel (ENaC). This generally provides a positive, attractive response, at least as has been demonstrated in mice. There are other, less characterised salt sensing cells and receptors, which were shown, by Oka et al, 2013, to activate neuronal pathways associated with bitter and sour responses, making these receptors intricately tied with producing an aversive response to salt. These findings demonstrate that the differentiation of a positive salty taste and aversive salty taste appears to occur on the molecular level on the tongue.

It is also important to note that recent studies have shown that there is no taste map on the tongue. Different tastes can be sensed anywhere, and it appears that some tastebuds may even respond to tastes other than the ones they’re designated for, if the molecules are present in high enough concentrations.

If the chemical signature of a piece of food comes back as being something which is not worth eating, then we may respond with aversion. This would be a basic explanation of how some kinds of taste aversion are generated.

For humans, this picture becomes a little more complicated due to differences in learning behaviour and intelligence. We actually enjoy some sour and salty and bitter things. In addition to the primal responses we can essentially learn to like or dislike something.

The mechanisms underlying perception of taste are poorly understood, but a general framework may work along the lines of context of tasting food. If peers express a dislike for a food, when one is first coming in contact with a food, this may influence a dislike for that food. Furthermore, knowledge of the benefits of the food may add a ‘top-down’ input of control over what one tolerates.

Our preference for food is regarded as a conditioned behaviour. The taste of the food is part of conditioning this preference. Additionally, the aroma and the texture of the food contribute to our overall perception of food. Generating a preference or aversion to a food involves more than just the specific taste, but shifts in preference may occur in response to different nutritional needs and differing social context of eating food. How the brain builds a conscious response to taste is immensely complex, and we’re only at the tip of the iceberg when it comes to understanding how this occurs.



June 27, 2013
Neuroscience could do with a Chris Hadfield

A friend pointed me to this article:

The article criticises the apparently negative reaction to the plethora of pop science ‘neuroscience’ books available and how it may be driving unhealthy scepticism of neuroscience research in general (a reasonable level of scepticism is always healthy). Some people believe neuroscience may be punching above its weight when scientists make such claims that understanding the brain will teach us the very basis of sentience itself.


I was reading about ‘Brainwashed: The Seductive Appeal of Mindless Neuroscience’ in last week’s issue of ‘Nature’. Yes pop neuroscience can sometimes be a bit of a problem (though not necessarily always). Some authors may look at inconclusive studies and make them seem like gospel and call it ‘SCIENCE’, when really it may just be a potential lead that requires more work and parallel studies. Either that or they’ll just quote a scientist and use that as proof for something. Quotes can be very useful at times. but just because an authoritative figure said something, it may not be fact. It could just be a view or opinion. There’s also the matter of confirmation bias which sneaks into a lot of this. Some authors may write their book with an agenda and this may drive where their ‘science’ is actually going, rendering it pretty much useless. It’s much akin to the early days of the very credible and verified sciences concerning evolution and heredity, what we now would call genetics. People would use insubstantial or misunderstood claims to back up false and often prejudiced views. I’m guessing as we’re still in the early days of dedicated neuroscience research, this could well be a typical reaction from people who aren’t used to this new field whose explanations could potentially be far reaching. I am very much of the thought that brain is mind, and that a lot of our behaviour, or products of our behaviour may well be explained by an understanding of how the brain works. I daresay this is more than a petty belief or hope, but a reasoned conclusion based on current evidence and understanding of neural function, (subject to change with advances in the field). It isn’t at a proven scientific consensus yet, but it is definitely one of the more logical conclusions out there that may be derived from current advances in the neurosciences and beyond. This very notion of brain = mind underpins psychiatric medicine and neurology. From neurosurgery to treat various neurological disorders, to how psychiatric drugs, or simply any drugs which affect the mind, work.

 But a great many people are uncomfortable with the notion that the brain may well be the mind because it questions humanity’s special place in the universe by shaking up the idea of ‘free will’ (just like Darwin’s theory of evolution by natural selection put humans in their place in the tree of life). In light of this some people try to do whatever they can to debunk it. People who misrepresent data to prove their own point or to sell books aren’t doing anyone any favours. What many people need to learn is, the conclusions we draw from science may not always be happy and to our liking, but objective evidence is objective evidence. It doesn’t necessarily matter what anyone believes about it (unless they have enough contrary evidence or flaws in experimental method to reason the other way)- if the evidence overwhelmingly points that way, then so be it. There will always be scientific ideas and discoveries out there that won’t settle well with many people. That doesn’t make them any less valid. One would hope any decent person would treat controversial scientific discoveries with sensitivity and morality. Because,well, nobody likes a douchebag (aside from other douchebags of course).

What would seem to be the issue is that there are some not so good pop science books out there which may be tainting what is an otherwise exciting, ambitious and highly relevant field in modern science. The brain and consciousness are frontiers of modern science, there is much potentially world-changing knowledge to be gained from pursuing the sciences concerning them. Also, some people out there may just not be particularly savvy when it comes to writing science books. They may lack the relevant tools of critical appraisal when it comes to researching the published literature and may have leading biases and agendas when writing their books, amongst other factors.

The best way of combatting this unhealthy neuroscepticism, in my humble opinion, is through more engaging and accurate outreach from the neuroscience, and indeed, the life science community in general. Neuroscience needs a Chris Hadfield, perhaps? There are other solutions, I don’t claim my idea to be the best and only, but I think some knowledge and charisma wouldn’t go amiss with modern audiences.


EDIT: Peer Review: As per some constructive criticism from the lovely onequantaaway, I feel obliged to add that  saying Brain =Mind is not to say the mind itself is the jelly like mass of neurons in the skull. The main concept here, to clarify, is that the mind is material in origin, and it’s genesis and functions should in theory (assuming we’re on the right track here) be traceable to physical brain functionality. my bad  for not being clear there, guys!

June 16, 2013
Neuro problems for a neuro man

It was a hot weekend, at least by UK standards. Home from work, as is the deal on weekends - working for the public sector has its advantages. I had been outside eating with the family. Nothing fancy. Then got straight to work on putting a roof-rack on my dads car (+10 man points). Nothing particularly fun. My hands got a little oily so I went inside to clean up.

I was washing my hands and felt weird. My left hand did an involuntary jerk while my right hand was clasped around it, and it felt so alien. I tried moving my left hand again but found it difficult.

I went to sit down, as a head ache set it. By this point, I had forgotten how to use my left arm. I would look at it, and but found it impossible to visualise how to move it. my right arm was fine. The head ache was localised to the right side of my head. I felt something warm on my left arm, and noticed i was drooling out of the left side of my mouth, without realising it. I tried to stand up to go to my room but toppled over onto the floor. My niece asked if I was ok to which I replied I was fine. I was having immense difficulty getting up as my left arm was out of use. the headache intensified. My brother tried calling me for more yard work. he came in to see me on the floor, my response to him was slow and my speech slurred. The drooling continued. I felt very undignified, lying on the floor, drooling and unable to get up. My brother thought i was trying to get out of yard work so threw an extension cable at me. My lack of a ‘fuck off’ response worried him and he called an ambulance.

The paramedics arrived swiftly and did various tests, concluded from my symptoms that I could be having a stroke and rushed me off to hospital.

In the ambulance I was vaguely aware of questions fired my way, and the distant wail of the siren. I also felt needles being poked into me. Something I have gotten quite used to what with my history of heart surgeries.

Once I got into hospital I was wheeled to a CT scanner. as I went in I mumbled something to the nurse about X-rays and EMI and ‘the legacy of the beatles’. She laughed, and probably figured I was delirious or something. How dare she jest at my expansive knowledge of Radiology history?! well not really. 

After some time, I was back in a ward, and was given some drugs and poked with more needles and had more blood pressures taken. I was informed I may have had an obstructed middle cerebral artery, and just had a transient ischaemic attack. Makes sense really. what with the left side not working and all. The basal ganglia in my right hemisphere may have been deprived of blood flow and thus wasn’t doing its job in coordinating my left arm movement.

After a couple of hours, and I began to sit up on my own, the hospital and staff really were insistent that I have tea and biscuits. How so very British, I thought. Tea and biscuits, the NHS’s cure all! I love it! I had to have some in the end, or just not hear the end of the offers for tea and biscuits. It was good tea. And the biscuits were good. I was glad for it.

Later that evening, with some help, I managed to hobble over to the toilet. This was good progress, and i was discharged shortly afterwards, with some medication and advice that I shouldn’t drive for at least a month. 

When I got home, I fell asleep almost instantly.

I was called in for an MRI scan and appointment with a neurologist later that week. The appointment was interesting, I saw my CT scan, and realised that it would most likely not show a whole lot as it was taken so soon after the initial attack - not long enough for the pathology to be detectable by CT scan, at least to my knowledge.

The MRI was interesting.I was actually looking forward to it! I turned up to the radiology department in Solihull with my Brother, and the radiologist was standing in the foyer waiting for me. She told me I may get warm in my jacket. I was like ‘NEVER FEAR’ and unzipped it, not realising I left the house without a shirt, and just wearing a jacket, exposing my bare chest to her. Exceedingly awkward. I mentioned that I may have forgotten to bring a shirt. She waved aside the notion and gave me a gown. It was cramped and hot in the scanner. I had to make an  effort to stay still. Most awkward when you have to scratch your nose. lying still in a hot and noisy scanner for 20 minutes isn’t exactly fun, but it certainly can be  interesting, considering this is a machine I studied quite extensively during my degree, and indeed it was invented at my alma mater. It was almost like meeting an old friend -  almost. Lying in there, I cast my thoughts to my protons, all being aligned by the powerful magnets. Strange thoughts crossed my mind, being restrained in this hot cramped tunnel. What if there was a murderer prowling around the room? and I did not know!? Not entirely sure where that thought came from! Kind of like when you’re in the shower and don’t know what’s on the other side of the shower curtain, I guess, and when you close your eyes, your imagination runs wild! Or is it just me? I’m not even superstitious or anything, this kind of shit just occurs. Darn introspective analysis! I blame my default Mode network! Either way, it ended without my murder, which is always a positive result, and I was informed I shall find out the result during the coming week. 

A scary experience all in all, coming face to face with something I studied in particular depth during my degree. Having a stroke at this age is most unusual; When I went to see the neurologist, everyone thought my dad was the patient and the nurse tried taking his blood pressure. It was most amusing. But the past week has  left me feeling weak and vulnerable. I hope to be able to get back to work soon and take control of my life once again.

May 6, 2013

So I just learned that Cleopatra actually lived closer in time to the moon landings than the construction of the Great Pyramid of Giza. Ancient Egyptian Civilization was around a very long time.

  • Pyramid of Giza — built circa 2540 BC (4553 years ago)
  • Cleopatra — Born ~69 BC (2082 years ago)
  • Moon Landing — 1969 AD (44 years ago)

  • Diff between Cleopatra and Pyramid of Giza - 2471 years
  • Diff between Cleopatra and Moon Landing - 2038 years

Shit son.


April 7, 2013
I’ve been neglecting you Tumblr, due to starting my new job - but you are not forgotten! Will be posting soon.
Came across this picture on reddit (titled: All of humanity minus one) and had to share. Genuinely gave me chills. Beautiful.

I’ve been neglecting you Tumblr, due to starting my new job - but you are not forgotten! Will be posting soon.

Came across this picture on reddit (titled: All of humanity minus one) and had to share. Genuinely gave me chills. Beautiful.

March 17, 2013
Goddammit entropy, give me a break already

Goddammit entropy, give me a break already

March 13, 2013
It’s a God awful small affair, to the girl with the mousy hair

Deviating somewhat from the standard theme of my blog, but it’s almost life-science related. Allusions to biochemistry and all that. Anyway, I’m sure most of you have heard the tantalising news of data emerging from the Curiosity Rover on Mars, suggesting that Mars had an environment conducive to life in it’s ancient past. I’ve had about a day to let that news sink in but it’s still exciting.

On facebook I follow a page called ‘The Universe’. It is probably my favourite page on that website. It doesn’t dumb things down, it keeps very true to themes about the universe and it’s not in your face and obnoxious like ‘I fucking love science’ sometimes gets (though it’s still a fun page to follow).

Regarding the recent data from Mars (the scientist in me is telling me to wait on confirmation data from the next set of experiments), ‘The Universe’ posted one of the most brilliant, beautiful summaries of the discovery on facebook. I felt it a bit of shame that it only went up on facebook, to me it bettered NASA’s own delivery of the gravity and implications of the discovery. Now let’s just hope the data presented by NASA isn’t anomalous (though all the cumulative data from Mars expeditions would make this somewhat unlikely)!

I like to keep the majority of the stuff I post on here original, and only reblog/quote in exceptional circumstances - and this is one of those circumstances. This is the excellent summary of the journey to find out if Mars could once support life, Copied from here. - 

 - “To tell that story, we have to go back to before the Mars Exploration Rover mission. When MER went to Mars, we sent 2 rovers, and we sent them to 2 different sites, both hunting for evidence of water. One went to a site that looked like a lake in the geomorphology, the other went to a site where orbital spectra indicated the presence of hematite, a mineral which likely formed in the presence of water. When we got to the two sites, we found the geomorphology site was filled with basalt, and the hematite-site was filled with sediments derived from a water-bearing environment. Eventually, Spirit caught up, and found evidence of a hydrothermal system, but really, the rover sent to the mineralogy site found the water first.

The Curiosity rover selection process was one of the most difficult decisions I’ve seen NASA make. Instead of 2 rovers, this time, they only had 1. They couldn’t miss. They basically had the same decision; picking between a mineralogical site and a couple geomorphology sites. The geomorphology sites resemble river deltas from orbit. The mineralogical site, a place called Gale Crater, had the spectral signature of clay minerals.

Clay minerals imply an environment we’ve never seen before on Mars. In very wet environments on Earth, clay minerals are the most important product. When a rock erodes in the presence of lots of water, the soluble elements are removed, and only the most insoluble elements remain. The 2 most insoluble elements in water are iron(III) and aluminum. 

On Earth, the continents are made of rocks like granodiorite and granite. These rocks don’t contain much iron, so Earth makes minerals that contain aluminum and water; aluminum-rich clays. Minerals like Kaolinite, aluminum clays. If you go to the Amazon River on Earth, coming out of a rainforest where water is abundant, the mineral you find coming out along with the water is kaolinite; water rich aluminum-clay. Clays tell you that the environment had a lot of water. They form in areas that have lakes and have oceans. They don’t form in dry settings, they don’t form in deserts, and they don’t form when water is only around for a short time.

Mars isn’t a granite world; it’s a basalt world. Compared to Earth, the rocks on Mars have much more iron. When you try to make clays out of these iron-rich basalts, the end result is an iron-rich clay called nontronite, rather than aluminum-clays. Seeing clay minerals implies not only that water was present, it implies a lot of water. It implies that so much water was present that all of the other soluble elements in the rocks were stripped out by water. This is a setting none of the other rovers saw, and this clay mineral was detected from orbit in abundance at Gale Crater. Quite simply, clay minerals are the #1 reason why the landing site was chosen. Last time, the mineralogical site found what it was looking for and the geomorphology site did not. So, with only 1 landing site, the mineralogical site, showing evidence of clay minerals and large amounts of water, was chosen.

The single biggest goal of this rover is assessing the rocks that contain clay minerals, the environment they formed in, and what that tells us about the environment on Mars when there was a large amount of water present.

That’s the backstory of this press release. Today, the Curiosity team announced the results of drilling into a rock called “John Klein” (drill hole pictured). The rover has been driving on what appears to be an alluvial fan deposit fed by a channel on the Gale Crater rim. The rover landed on coarse grained fan rocks, and drove to a place where the rocks appeared finer grained. These fine grained rocks are the rocks they drilled. 

They fed this first drilled sample into the CheMin instrument and the SAM instrument. CheMin is an X-Ray diffraction system. It is spectacular at identifying minerals. If you wanted to identify clay minerals, it’s exactly what you’d want. They fed the drilled sample into CheMin, and…it turned out to be made of iron-bearing, smectite clays. Also known as; nontronite.

They also fed the sample into the SAM instrument, a mass spectrometer. SAM can measure abundances of elements like carbon and sulfur, and hopefully also measure isotopes on those samples. They didn’t give us the isotope compositions in the press release, suggesting that they’re still working on those, but they did announce the presence of carbon and sulfate bearing minerals. 

Put all this together, and the most important part of today’s results is this sentence; we found what we were looking for. In the other 2 sites on Mars, we found evidence of some water, but not large amounts of water. Spirit found a hydrothermal environment, where small amounts of water circulated through the rocks. Opportunity found an oasis in a desert, where small amounts of water had moved through rocks and precipitated minerals like hematite. 

Curiosity went to a place where the orbital spectra say there should have been a lot of water. Clay minerals aren’t made when there is only a small amount of water; it takes a lot of water to make clay. It takes a lake, or an ocean, or at least long-lived water bodies. The other rovers found small amounts of water and the signatures of acidic environments.

To create a habitable environment, as we understand it, you don’t just need small amounts of water, you need a lot of water. You need enough water to drown the rocks, to move most of the elements around. The end result of this amount of water should be clay minerals. If that kind of environment ever existed on Mars, the signature should be nontronite clays. Those clay minerals could be trapped in mudrocks, like shales and siltstones on Earth, and if we’re lucky, they’d have carbon, sulfur, and other elements that life could make use of trapped within them that could be analyzed.

That rock type is…exactly what Curiosity drilled. We went to Gale crater hunting for clays. We picked Gale Crater because orbital spectra said there was clay. We wanted to see the rocks that hosted the clay, measure the chemistry of clay-bearing rocks, and interpret what the environment was that formed them.

There are a lot of other interesting details about this rock. It appears less-oxidized than the surface. It isn’t fully red; when they drilled the rock, they found it looked dark; meaning some of the iron hadn’t oxidized. It wasn’t fully altered. They also found olivine, an easily-erodible mineral, in the mudrocks. These results suggest that the clays were laid down with sediment that wasn’t as highly altered, because olivine and reduced minerals wouldn’t survive that much exposure to water. They also found both sulfates and sulfides, indicating partial reaction of the sulfur-bearing minerals, but not complete consumption of them. These details will take time to figure out, and I’m sure the team will target a whole lot of effort to figuring them out, as chemical reactions involving reduced minerals and sulfide minerals on earth provide energy that life can use to sustain itself. 

All of these are important and the team will keep working on them. But the message you should take from today’s press release is this; we went to Gale Crater looking for clay minerals like nontronite in the rocks, because those minerals would tell us that there was a very large amount of water when they formed. Today, they announced…they found what they are looking for. Curiosity is where it was supposed to be. We sent an organic chemistry laboratory to Mars to look at clay-bearing rocks. We now have an organic chemistry laboratory sitting on clay-bearing rocks. We found what we are looking for.


imageImage credit: NASA/JPL-Caltech/Cornell/MSSS

The image compares rocks seen by NASA’s Opportunity rover and Curiosity rover in two different areas of Mars. On the left is “Wopmay” rock, in Endurance Crater, Meridiani Planum, studied by the Opportunity rover; on the right are the rocks of the “Sheepbed” unit in Yellowknife Bay, in Gale Crater, which Curiosity has been studying. The images have been white balanced to show roughly what they would look like if they were on Earth. ” -

February 10, 2013

The medical library of my alma mater, The University of Nottingham would sometimes give away books it didn’t need anymore.There’d be a shelf by the door with the unwanted books which students could just take for free. On one occasion, late at night just before the library closed up, I was on my way out when I came across these gems. Scientifically they’re not of much use, but as historical documents, showing how scientific perspectives on the brain, behaviour and the mind have changed, these are positively fascinating.

The oldest book I obtained, ‘On the Constitution of Man’ is pre-darwinian and pre-mendelian, and attempts to discuss the role of humans in nature based on recent advances in the understanding of natural laws. An interesting chapter in it is where it tries to tackle the notion of heredity. The author notes the flow of characteristics from parents, be they diseases (which we now know to be genetic diseases), or traits such as skin colour and body build. It is interesting how the author attempts to explain how this works, through the use of medical literature available to him and through his own observations and rationale. Though he somehow ends up at the conclusion that more hereditary influence comes from the father. I guess it’s just a sign of the times. We are talking 1820-1840’s here afterall. Another fascinating aspect of the book is how it reflects the struggle to reconcile the wealth of science regarding the fundamental laws which structure life and the universe, with religion. It talks about natural laws present in animals also applying to humans, yet it tries to put a theological spin on it. It is fascinating how around 30 years later this idea would change.

The book on physiognomy was a book on the science behind human expression. It was very interested in how expressions differ, or are similar across different races. This book was pretty far-out, even for the Victorian period, making some references to telepathy and other bogus notions. It was a rather racist book, though once again I imagine it is little more than a product of its’ time.

This collection of books, though thoroughly outdated (and somewhat unintentionally racist at times) is truly marvelous  A brilliant insight into the evolution of science and the influence of culture during a time of great change in attitudes towards science. The book written in 1869 actually makes some reference to Darwin, showing how much of an immediate influence his landmark works on Evolution had. Thank you Nottingham for these gems.

February 10, 2013
The Anatomy of Reality


Psychosis principally consists of ‘reality distortions’. A person exhibiting psychosis has a skewed perception of reality - the result of faulty circuits in the brain which are involved in perception. Reality distortions are typically characterised by hallucinations and delusions.

Psychosis can occur in isolation, but usually occurs with other symptoms which together form a psychiatric syndrome. In a syndrome, patients exhibit a cluster of symptoms which individually could be seen as distinct disease states. Examples of such syndromes include bipolar depression, major depressive disorder and schizophrenia. Many patients do not exhibit the same set of symptoms. They probably share the same defining hallmarks of said disease, but also have other more variable symptoms alongside. These ‘extra’ symptoms complicate matters, as they usually arise from dysfunction in a different system of the brain, which could require a different course of therapy.

Schizophrenia is a psychotic syndrome. It is characterised by the presence of

positive symptoms’;  The psychosis. Psychosis is one of the defining and more recognisable symptoms of schizophrenia

negative symptoms’; Social withdrawal, decreased spontaneous speech, apathy, self-neglect and decreased emotional expression (flat affect).

Many of the neural circuits involved in perception and attention use dopamine as their neurotransmitter.  Dopamine is not exclusive to perception circuits, and neither are all perception circuits dopaminergic – but the point is there’s a lot of dopamine involvement.

There are 4 main dopamine pathways in the brain; mesocortical, mesolimbic, nigrostriatal and tuberoinfundibular.


The diagram hasn’t labelled the tuberoinfundibular pathway, though it is highlighted as the small pathway starting from the hypothalamus. Diagram from ‘Dopaminergic neurons’, Chinta & Anderson 2005, The International Journal of Biochemistry & Cell Biology

All of these tracts originate from roughly the same brain region. This region includes the structures involved in reward and motivation. The pathway of note in psychosis and perception is the mesolimbic (and to an extent, the mesocortical). In schizophrenia, the positive symptoms (psychosis) arise from excessive dopamine function in the mesolimbic pathway. Drugs which block dopamine neurotransmission are used to combat psychotic symptoms. Such drugs include haloperidol and aripiprazole; useful chemicals which bring perception back in tune with reality, removing hallucinations and bringing delusions down to a tolerable level.


chemical structure of Dopamine

A hallucination is a seemingly realistic perception which occurs without any sensory input; seeing something which isn’t actually there, but having no idea that it isn’t actually there. It is as real as your own two feet in your own thoughts, though objective evidence from the world around you would suggest it wasn’t there.

Hallucinations are thought to arise from impaired wiring in neural circuits involved in perception. One theory suggests that the neuronal networks involved in imagination are misconnected to the circuits involved in processing incoming sensory information into perception. As a result, thoughts which would be the domain of imagination are ‘perceived’ as information directly sensed from the environment. Electrophysiology studies using EEG to measure brain waves support this theory by showing aberrant electrical patterns from such sensory-to-perception circuits. The theory makes sense (and is one that has my backing, if it’s worth anything) given the nature of hallucinations, and it has reasonable evidence to back it up making it a strong candidate to explain, at least in part, how hallucinations occur. Neuroanatomical evidence to back this up is complex, with different regions involved depending on what sort of hallucination the person is undergoing. However, the impairments which give rise to hallucinations are only part of the story of psychosis.

A delusion is defined as a fixed belief derived by illogical reasoning or unjustified assumptions that cannot be explained by culture or religion. At the crux of a delusion is a premature conclusion - seeing a trend before enough information to rationally describe a trend has been presented. Delusions are generally culturally influenced, with delusions of old consisting of stories about ghosts and demons (stories which do still exist) to more modern delusions which involve government conspiracies and aliens. The cultural context of the story is variable, but rests on fixed, illogical conclusions which cannot be swayed by contrary evidence or reasoning. This sounds like a complex behaviour as opposed to a symptom of a disease state– but the real behavioural pathology here is the fixed misinterpretation of information to jump to early, and absolute conclusions.

The biological basis of delusions, which should hopefully begin to explain their role in psychosis, lies in a phenomenon termed by those in the field as ‘aberrant salience’. Normally at the level of neuronal computation, the brain makes predictions about events in the environment, and when such an event does not meet the prediction, dopamine is released in regions of the brain which drive reward and salience. There is a network of neuronal circuits in the brain called the Salience Network. The Salience Network is involved in influencing attention to environmental events. The salience network uses dopamine neurons (amongst others), and when the dopamine neurons in the salience network are active, they activate neuronal networks involved in drawing attention to this stimulus, and this begins analysis of the novel event – which will thus drive perception and thoughts of this new, interesting event.


Diagram showing regions of brain part of the Salience network and Central Executive Network. The Salience Network regions are highlighted in red and orange. Images obtained from fMRI neuroimaging. Diagram adapted from “Large-scale brain networks in cognition: emerging methods and principles”, Bressler & Mennon 2010, Trends in Cognitive Sciences

In a delusion, this dopaminergic system appears to be impaired, resulting in salience being attributed to irrelevant cues in the environment. This would imply excessive dopamine is being released. The theory put forward by Andreas Heinz and the various members of his research teams asserted that environmental stresses could induce ‘chaotic’ dopamine release in these systems, responding to irrelevant events as if they were relevant. This would lead to the formation of a thought or conclusion about a given event that was based on irrelevant or misleading information. This theory is supported by a wealth of evidence from rodent, primate and human studies. Such studies include verifying that social stress plays a role in dysregulating dopamine release in primates, and pharmacological and neuroimaging studies in humans has shown that ‘chaotic’ dopamine signalling can affect reward-prediction processing. In schizophrenia, there is already a malfunction leading to increased release of dopamine, so this would explain the existence of pathological delusions in the absence of environmental stressors in line with this theory.  More research is needed to conclusively verify this hypothesis of chaotic dopamine, but the trend of evidence is very promising.

Transient psychotic symptoms can be induced by some recreational drugs as part of their action. Such drugs include cannabis, amphetamines and cocaine. There is verified experimental evidence for acute transient psychosis (psychotic symptoms brought on during drug use) from cannabis and amphetamine, and population based evidence for such symptoms from cocaine. Long term use of cannabis, amphetamine and cocaine is associated with the development of a psychotic disorder later in life, but the there is great debate as to what the causation to this correlation is.


Chronic use of cannabis is thought to inhibit the generation of new neurons in the brain so it is possible that cannabis usage can interfere with brain development, leading to some miswiring events involved in psychotic symptoms. With brain development occurring well into the teenage years, it is thought that cannabis use may precipitate schizophrenia or psychotic disorder in teens who have a genes which make them susceptible to such disorders. Amphetamines and cocaine interfere directly with the dopaminergic pathways, and their role in producing psychotic symptoms during drug use is much more straightforward. Amphetamines directly increase dopamine function so by looking at their very chemistry and pharmacology, their predicted effect would be something similar to psychosis.


Psychosis and the effects of drug use on the brain demonstrate just how material our thoughts, emotions, personalities and memories are. They can be seen as another part of our body. This line of thinking should hopefully allow us to understand those who suffer from mental health issues. It shows that mental health disorders are a very real phenomenon, and not just people trying to be awkward. Such disorders are leading scientists to question the very nature of free will itself. Psychosis and the predictable effects of drugs on the brain are striking evidence of just how chemical we are at the deepest level of what we see as our soul.


February 9, 2013

I was bored, and it was a rare occasion on which I had the house to myself, so I decided to put on the old webcam and just… talk about the first thing that came to mind. So here’s me on my soapbox, giving a pointless perspective on Social Justice on the internet.


January 25, 2013

Anonymous said: Hey I saw your post about Kallmann's Syndrome and I just wanted to say its very informative and well written :) I am a female with Kallmann's but I have been treated so I did get my period but I don't have boobs and I can't smell.

Good to hear about the treatment, I’m glad my post was informative, and thanks for the compliment! I sincerely hope things continue to improve for you! :) Rock on!

(to anyone who’s interested, here’s my post from way back in early 2011:

January 25, 2013

jung-yunho said: Good thing my name ISN'T actually Haseeb. >:

Nice try, impostor

January 24, 2013

jung-yunho said: Hello. My name is Haseeb too.

You must be neutralised. Only one can live.

Liked posts on Tumblr: More liked posts »