Thursday, 18 August 2016

Why is the sea salty?

This is a long standing request that I have been waiting to do, although I wasn't quite sure I had that much to say about it at first. But before we get to why the sea is salty now and how salt is left behind when water evaporates, lets talk about how all that salt got into the sea in the first place. Better yet, how did we even get seas for there to be so much salt in anyway?

Cast your mind back say 3.5 billion years, give or take, when the world was just forming into a huge molten rock. In those days, Earth's early atmosphere contained a lot of hydrogen and probably quite a lot of water vapour too, as oxygen and hydrogen bond readily to form water. But, as the earth was a giant volcanic molten mess at the time, the surface and atmosphere were far too hot for liquid water. As you may know, boiling points are subject to conditions such as pressure (that's why rapid boiling tubes use a high pressure, like in a coffee machine) but also the composition of the atmosphere, which was losing hydrogen through the power of the Sun. The sun's energy can split water into oxygen and hydrogen, which then can escape earth's atmosphere and the relative amount of oxygen compared to water increased. I don’t quite understand why (probably something to do with pressure) but apparently this caused the temperature at which water remains a liquid to increase

As the boiling point of water rose until it hit the 100 degrees Celsius it sits at today, the temperature of the atmosphere gradually fell as the earth cooled. Eventually the temperature of the atmosphere dropped below the boiling point of water, and you have rain. Lots and lots of rain.

While the atmosphere may have been cool enough for liquid water, the surface certainly wasn't. As the train fell and was immediately turned back to vapour it slightly cooled the rocks, and as it turned back to liquid high up in the atmosphere the heat it had gained was eventually lost to space. This cycle could have easily continued for a million years until eventually most of the water on earth was liquid. The water then pooled in the lowest lying regions in the earth's surface to form the oceans.

So how did the sea get so full of salts and other minerals?

There would have been (and still is) a lot of dissolved carbon dioxide dissolved in the early oceans, which is acidic. Other acids like hydrochloric and sulphuric acid may also have been around too. These acids ate away at the earth's rocky surface, gradually adding salts and minerals like common salt and calcium. When life came about, these minerals were put to use. Calcium carbonate salts are used for producing hard shells and coral reefs and sodium chloride salt was used to form the very first nervous system (or possibly potassium chloride, they're is some debate). Even now, in all animals, salt is vital for the functioning of nervous systems and a lot of energy goes into maintaining the perfect balance of sodium and chloride ions dissolved in various cellular and extracellular fluids for optimal performance of the nervous system.

So now we have seas and we have salt, now all that's left is how the salt stays dissolved in the sea when the water evaporates. In essence, salt transitions to a gas at a much higher temperature than water, so water can evaporate at the sea's surface when warmed by energy from the Sun much more easily than salt, which is left behind.

To go a little deeper, common salt molecules are made up of one sodium atom (Na) and chlorine atom (Cl) to make sodium chloride (NaCl) – the salts in the sea are much more varied than that, but for simplicity let's just talk about common old table salt. The two atoms are normally bonded together by ionic bonds; because an Na ion has a positive charge (Na+) and a Cl ion has a negative charge (Cl-) . For salt to dissolve in water, water has to interact with salt molecules more strongly than salt interacts with other salt molecules. As the interactions between different salt molecules is weaker than their interactions with the many many more water molecules in the sea, salt dissolves and dissociates into its component ions (Na+ and Cl-) so that the Na sits on the slightly negative oxygen side of a water molecule and Cl sits on the slightly positive hydrogen side and the ions from the salts become mixed between the water molecules.

As you can see in this image, it is not just one water molecule required to dissolve one molecule of NaCl, but many. Apparently the minimum number of water molecules required to dissolve NaCl is between 9 and 6 for one salt molecule. If you want to get a little more complex you can start to talk about free energy. Essentially, the balance of energy used up by breaking the ionic bonds in the salt crystals and the energy released by forming new polar bonds with water works out in favour of dissolving the salt crystals - and so they dissolve.

Why does salt remain in the sea when water evaporates?

When the sea is heated by the sun, the water molecules gain energy and are able to turn into vapour (called a phase transition) much more easily than salt ions and therefore water evaporates and salts don’t in those conditions.

When the evaporated water eventually cools and rains on land somewhere, it eventually makes its way back to the sea and picks up lots of sediment full of salt and other minerals. Some of this sediment makes its way to the sea and can be used up by all sorts of sea creatures to form their shells or just fall to the sea bed and eventually form sedimentary rock as it gets compressed over many thousands of years.

If you boiled away all the water, you would eventually find that the salt began to reform salt crystals. This is because, as there is less and less water, it has now become more energetically favourable for the component ions to start reforming salts and to form a precipitate; the equilibrium of dissolved–precipitated salts shifts towards the solid precipitated salts. This is sort of what is happening in the Dead Sea, which has an incredibly high salinity, but it's more likely that a load of salts have been deposited there and they’ve just accumulated.

So there you have it, how we got seas, how they got salty and why they remain salty today. Thanks for reading.

Thursday, 30 June 2016

Take a look at how the visual system works

You probably never really thought about this before, and neither had I really until I read about it about a month ago. But it turns out that your eyes are pretty much the least important player in vision. You might be pretty sceptical at this point, so I want you to close your eyes and imagine a boat. Done it? Okay, good, you just saw something without using your eyes!

At this point, you're probably wondering where I'm going with this. ell I'm about to show you how much work has to be put in to be able to see something properly and hopefully you'll realise just how impressive the machinery  in-between your ears really is.

First, let's start with how we can go from an array of photoreceptors in the retina to a complex image of the world around us in 3D. First you have the two types of photoreceptors in the primary visual system; rod cells can detect low level light but they do not give very good acuity and they do not give colour vision, cone cells can detect colours and have very good acuity but they need high levels of light intensity. When these photoreceptors detect light, they send a signal to an area called the primary visual cortex (PVC) at the back of your brain, which you can see below.

Visual cortex Picture Slideshow
The primary visual cortex (PVC) sits just at the back of the brain, with much of the occipital lobe devoted to visual processing in some way.

The PVC deciphers the signals that came from your retinas, works out what's in your field of vision and then sends the signals to numerous other places within your brain focused on memory, decision making and anything else that could create your "conscious awareness of the world". This all occurs within around 200 milliseconds, pretty impressive right?

To create a visual representation of our world so quickly, our brains use a number of assumptions about how the world works so that it can take shortcuts. For example, because we want to be good at spotting other humans and also predators our brains are primed to spot these faces everywhere. Because of this face bias, we are prone to seeing faces where the do not really exist (Jesus on your toast, anyone?). If you want to learn more about these assumptions, look up Gestalt psychology. 

The assumptions our brains make can sometimes be wrong, I'll put down a few examples below, but we've all got our own favourite visual illusions so please post a link to your favourite in the comments if you like. 

This is no photo shop manipulation, but a real room with such a crazy layout that when girls of the same height stand in different corners they appear to be completely different heights. Hint: the bigger girl is higher up and closer to the observer than the smaller girl.

If you look at this mask you'll quickly see that when you look at the back of the mask, it suddenly appears to be pointing out towards you and spinning in the opposite direction.

So now you can see that while it's easy to pick up information, deciphering it requires much more work and we have very sophisticated systems to allow us to create a very vivid and detailed picture of our lives. You really see just how impressive this is when you step away from 2D still images and move on to 3D moving images. Because you're dealing with so much more information with moving images and real life, your brain has to rely on its assumptions and strategies (eg selective attention) even more, which can greatly influence what you notice, try this video below to test out your selective attention abilities.

Here your brain is focusing on one small element in a scene, leading us to miss some pretty obvious goings-on within the rest of the scene. Now this isn't just a clever lab trick or an amusing video, this happens all the time in our daily lives (obviously we don't notice), as you can see from this final clip.

What is out there to be seen and what we actually see are completely different- and they are massively influenced by our consciousness.

If you want to learn a bit more about the neuroscience behind how vision works, this is a good starting point. Also check out this website for a really great tool that allows you to easily see the power of the visual system. 

I hope that I have illustrated the real processing power of the human brain and how easy it can be to understand a little bit more about what is going on behind the scenes in our brains.

Please feel free to comment, share or follow this blog and I'm always open to topic suggestions.

Friday, 8 April 2016

Combat Dolphins and Rocket power measured in Elephants: the most weird and wonderful articles in March

With another month down, I can proudly announce my roundup of the most interesting articles I read in March is here! 

If you think any of these articles deserves more coverage, please leave a comment and I'll probably write an article about it just for you – I'm nice like that! 

Let's get to it...

Should young scientists be fighting for their employment rights the same way junior doctors are?

Young scientists are caught in the middle of student and professional and are therefore treated as a hybrid of both - expected to work 24/7 but for very little money and recognition, relative to their contributions.

How many Elephants worth of energy does a rocket launch use up?

Because why the hell not?!?! Turns out it's quite a lot... 

This comic almost perfectly illustrates what has happened to Twitter

Turns out Russia and the USA use Combat Dolphins

Yep, you read that right...

Apparently in Japan there's a trend towards choosing partners based on whether your blood types are compatible

Helpful note: your blood type has NO influence on your personality in any way!

Flies could theoretically falsely place someone at a crime scene 

I hope the writers of the show 'The people vs OJ' have seen this... 

Driverless cars have been in a few scrapes, but could they survive a fatal accident?

Driverless cars have received fairly reasonable coverage over the one or two minor bumps the cars have been involved in (only one was the car's fault) but how the new technology weathers its first fatal accident could make or break this technology.

Despite a misleading press release no, scientists have not created a way to instantly upload knowledge to the brain

What they actually did was measure the brain activity of expert pilots in a flight simulator and then tried to improve performance of novice pilots in a simulator by stimulating their brains in an attempt to mimic the brain activity seen in the expert pilots. Turns out the researchers had patents pending on the technology used and the test subjects were employees of the company that produced the tech - what conflict of interest???

What if you channeled Niagara Falls through a straw?

It would end very, very badly...

This was a very weird month for science articles. I'm sure normal service will resume shortly – although I hope it doesn't!

Friday, 1 April 2016

How can we measure individual brain cells in real time?

The ability to identify and control individual brain cells (neurones) has generated huge interest in recent years, it's made for some startling discoveries and some incredible images (like the one below). But we're really only beginning to scratch the surface of the potential these technologies hold, and the techniques here are quite controversial. 

This is a real image of individual neurones and the connections they make, all with individual colourings 
The actual methods for controlling individual neurones require a lot of complex genetic manipulation, but the general concepts are easier to get to grasps with. The main method used for the genetic manipulation of animal genomes is the cre-lox system. I won't go into the details (you can read a great review by its inventor here) but this technique allows scientists to insert or remove any gene you want, in any cell, even at specific times (when the cells are still growing or mature for example). 

The next question many people then asked was, what if I can use this technique to influence an animal's behaviour? Specifically with neurones, could I activate or inhibit the electrical communication between neurones in real time in a real life behaving animal to study the effects of individual sets of neurones on behaviour e.g. learning, memory, reflexes, social interaction, etc?  

Turns out, yes you can! The most well known and fashionable technique at the moment is called optogenetics, but there are a couple of other interesting methods, which I'll explain below. The general idea is to insert a gene into the neurones in order to make them sensitive to a stimulus which there are no (or very few) cells that are sensitive to it in the brain and is also able to manipulate or monitor the electrical activity of the neurone (these are almost always ion channels, see here for how ion channels cause neurones to 'fire').


As you may guess, this involves using optics ie light. By inserting genes for a light sensitive protein that can activate or silence neuronal signalling activity into neurones and applying a light stimulus by using tiny fibre-optic cables, you can control electro-chemical communication between the cells at millisecond time scales. 

A tiny light on an individual neurone causes a change in the behaviour of the neurone.

While this technique offers incredible time resolution, however it's incredibly invasive (you have to insert the fibre-optic fibres into the brain of the animal) and incredibly difficult to get right (you need to make sure the fibres are actually lighting up the neurones you want them to). This creates a huge problem if you want to target neurones deep within the brain, as you need access to those incredibly tricky to reach parts of the brain. 


Another cool way scientists have been able to manipulate the brains of animals using genetics have involved the use of chemicals, or toxins to be more specific. Researchers have used the Cre-lox system to insert the gene for various toxins eg a fragment of the diptheria toxin into specific neurones in order to kill those cells and observe the effects this has on the mice. Although a bit crude, this can help to identify the brain regions involved in all different types of behaviours, and could help us understand how the brain reacts to and compensates for the loss of specific regions of the brain eg after stroke, dementia, trauma. 


This technique doesn't necessarily allow researchers to directly manipulate neurones, but it does allow us to watch the activity of specific cells in real time. By inserting genes that express proteins that emit a flourescent light when they sense changes in voltage (indicating electric activity in the neurone) we can easily see each neurone light up individually and trace which other neurones are activated or de-activated by that neurone. 

This video below used this technique to show how individual neurones in the auditory cortex are firing in response to sound. 

Along the same lines, you can insert specific genes across the entire brain that randomly express a different ratio of red, green and blue fluorescent proteins. That means that each individual neurone has a unique colour, which gives rise to the incredible 'brainbow' images seen above. 


This very new method of manipulating neurones involves inserting a gene for an ion channel protein that is activated by magnetic fields you can instantly turn neurones on or off or block anything else from activating it (ie other neurones) while the animal is relatively free to move around and act as normal, without needing a bunch of fibre optic cables delicately positioned in their brains. The fact you don't need to worry about exact positioning of any equipment means that much deeper brain regions or much more specific neurones can be manipulated than with optogenetics. There may also be potential for more analogue control of activity by using a weaker magnetic field that only slightly affects the activity of the neurones being manipulated. However some neurones are already sensitive to magnetic fields, birds and other animals can use them to navigate by, for example.

I couldn't not use this picture once I found it!


Probably better named audiogenetics (although we can't hear ultrasound...), there is also some very early research into making specific neurones sensitive to ultrasound. This would have many of the benefits of magnetogenetics and both could be the future of genetics based neuroscientific research in animals. 

Clearly, there are a number of new and emerging ways in which researchers may be able to investigate the role of very specific neurones in the brain. While some may be initially put off by the idea of manipulating the brains of animals, by understanding these very specific roles, we may eventually reach a more complete understanding of how the brain works and how to fix it when it goes wrong. 

Friday, 11 March 2016

The Productivity Project: what I learned from reading a book about productivity

I recently finished reading a book called The Productivity Project, by Chris Bailey. It’s doing well on amazon and receiving great reviews on goodreads (4.1/5 stars on average).

I thoroughly enjoyed reading his online blog about his yearlong productivity project, in which he tried a number of experiments on himself to see how they affected his productivity such as working crazy long or short hours, eating nothing but Soylent, waking up at 5:30am every day and many more. What I liked most about this book, is that it’s incredibly down to earth and written in a very accessible and positive way. Chris talks about his own successes and failures openly, he shows you that achieving productivity isn’t something that only superheroes can achieve and even does a good job of explaining the psychology and neuroscience behind the secrets of productivity and behaviour in an accessible way that doesn’t dishonour the science.

He also includes a number of tasks and challenges within the book, to help you to truly engage with the ideas he puts forwards, as the whole point of reading a book about productivity is to try some of it out, right? So I’ve put together some of the things that have stuck with me a month after I finished reading the book.

Align your productivity goals with your values
The first, and arguably most important strategy from the book is to make sure that what you aim to achieve matches up with your values. Maybe you want to get a raise, why? Is it because you want to further your career, or is it because you need the money to buy a house and start a family? Maybe you want to work shorter hours, is this because you’re feeling burnt out or because you want more time to see your friends and family? By identifying why you want to achieve something, you’ll be able to stick at it better when your initial wave of motivation inevitably leaves.

Focus on your most important tasks during the day
You might have heard of the 80-20 rule, which says that 80% of your value comes from 20% of your tasks, so by focusing on those tasks you can maximise the value you contribute. You should also try to avoid multitasking when working on your most important tasks and work deliberately, rather than just on autopilot.

Set 3 daily intentions, and follow through with them
This technique stuck with me immediately, and I have no intention of giving up on it now. It also follows on well from the previous lesson. Chris suggests to write down 3 things you will accomplish each day and they do them. The wording is important, rather than just 3 things out of your to do list or 3 things you’re going to work on, its 3 things you’re going to get done. I also find it very useful to start each intention with a verb eg finish or send or research. You can also set intentions for what you’ll do outside of work and even some broader intentions for the whole week. It’s also important to check up on how you’re doing throughout the day and to let yourself feel good when you get everything you aimed to accomplish done in that day.

Recognise when you feel resistance to a task and work to minimise that resistance
We all have jobs we don’t want to do, or we’ll get to another time. Chances are its unstructured or boring or just really difficult or even a bit scary. By recognising when you feel resistance to a task and then working towards shrinking that resistance, you’ll be able to stop procrastinating on those tasks you really don’t want to do but know you need to do. Some ways of lowering that resistance are; only commit to working on it for a short period of time until you feel less resistance to it, make the task more interesting or more structured, ask for some help and set yourself a reward for once you’ve finished the task to pat yourself on the back.

There are many many many more tips and techniques in the book as well. But the best parts of this book were the personal stories along the way, you really get to see into his world in a delightful way and he always insists that any changes to your life that you make have to work for you and aren’t just ‘productivity porn’ like getting up at 5:30am just because you think that’s what productive people do. 

Friday, 26 February 2016

Top articles of the month

This is the first in what I hope will be a regular round up of some of those articles I add to my "to-blog-about" list that never make it to realisation and a selection of articles that I thoroughly enjoyed and recommend everyone reads. I've added in a quick summary of the articles, as some are academic journal abstracts, but you should still follow the links and read the full thing, especially the first two!

What if? Can we use satellites to stop the orbit of Jupiter?

Again, the What If? series is one of my favourite and funniest things to read, especially as I am not a physicist (although I do think it's pretty awesome to learn about). This latest question is about how using Jupiter as an effective gravity sling-shot for satellites affects the orbit of Jupiter. Just read it, I loved it!

We have no idea why humans have chins...

Ed Yong is easily one of my favourite science journalists, and this article explains a lot about why I like him so much. Apparently, we are the only animals that have chins ie a bone jutting out from underneath the jaw, load of animals have lower jaws. We also have no idea why we have them, or what evolutionary purpose they may have served (if any). Some of the ideas about the origin of chins are a bit weird, and very entertaining!

No evidence for link between Microcephaly outbreak and pesticide in Brazil

Snopes does a great job of explaining what we know is true, what we know is false, and what still remains to be determined around the Zika virus. What is certain, there is no credible scientific evidence to link the cases of Microcephaly in Brazil with the use of the pesticide pyriproxyfen. 

Effects of playing Fifa 2015 on stress and cognition

It's always good to see an article about the effects of video games on the brain. This one studied the effects 32 20 year old healthy males playing Fifa in Iran, making a change from the usual shooter games in the US. They found that cortisol (a stress hormone) levels significantly reduced after playing the game and there was no mental fatigue from playing the game. The investigators also measured EEG but I won't go into that in detail as they are somewhat unclear on the outcomes.

You often hear about crowds bystanders failing to act when someone is in trouble, I'm sure we've all seen it first hand to varying degrees. This study shows that due to the effects of alcohol on social inhibition, people more quickly came to the aid of others after a few beers. In my opinion, this one looks like an excuse to head down to the bar for "research purposes". You'll also be pleased to hear that this study was conducted in Amsterdam, not jealous at all...

Pharma Company reports failure to reproduce academic studies

We've all seen hyped up articles in the news about how some 'breakthrough' could be in clinical trials 'within 5–10 years and then no-one ever hears about it again. When an academic pre-clinical (before testing in humans) study makes these kind of waves in the news, you can bet your house that at least on Pharma company will be trying to reproduce those findings to find the next wonder drug. Unfortunately, when they are unable to reproduce those findings it often goes unreported. Amgen have started to publish these results and hope that others will follow their lead. A failure to reproduce does not mean that the science is wrong, just that the techniques, conditions etc from the original studies need to further development in order to become robust enough to make a viable treatment for disease. 

Wednesday, 17 February 2016

Changing from student life to real life

This is the second post in this series of posts about making the transition from university life to 'the real world'. You can find the first post, about starting out at university here. I've been outside of the student lifestyle for about 8 months now, and I've had the fortune of finding a job that works well for me. But it always takes time to adjust to a new stage in your life, so here are a few of the major changes I've noticed since I left university, mostly for the better!

Fewer people your own age in the workplace

Unless you're recruited as part of a company with a huge graduate program or you work in some sort of start up or digital tech business, you probably won't find too many people your own age in the workplace. This can be a good thing and it can be a bad thing. By mixing with people of different age groups you get new perspectives on things and get to see the bigger picture outside of the student bubble we've all been living in for the last few years. 

The downside is that, because you are at completely different life stages to most people, it can be more difficult to connect initially. Although, I've found that after a while you can overcome this initial boundary and make friends quite quickly once you find some common ground!

The commute

Unlike when studying at University, it's fairly unlikely that you will work within walking distance of your home. So you'd better be prepared for a fairly lengthy commute. Mine is about an hour, with 25 mins walking and 35 mins on the train (if everything is running on time). That's a pretty good commute from what I've heard, and most of it is spent moving, which helps you to feel like you're not wasting time during your commute. 

One recent study found that walkers had a significantly less stressful commute compared with travelling by car- followed by people who used public transport. Interestingly, the most enjoyable part of the commute for people using public transport were the short walks between transport links! If you do get stuck in traffic on the bus or your train is delayed, you can just sit back and read a good book.

I've been enjoying the DiscWorld novels by Terry Pratchett and I'm about half way through the entire DiscWorld collection since I started working in June! Obviously this is not possible for everyone, but if you can avoid the extra stress it is well worth the money and, depending on your route, it may be even cheaper than driving.  

Free time

The way my free time has changed is quite drastic. As a student, free time was just time when I wasn't studying or doing something productive. This could have been lying in, chilling out during the day or staying up into the small hours of the morning or binge watching something on Netflix and generally being lazy. 

I've since realised that this kind of prolonged procrastination is only enjoyable when there is something else you should be doing instead! Because now, although I have less free time, a lot more of it is time when I can freely do whatever I want. That means that things like binge watching, video gaming and generally slobbing out are still enjoyable, but not for the entirety of my free time. These things no longer have that sense of guilty pleasure, and I feel like I'm not 'making the most' of my free time when I use up all of it on these guilty pleasures. 

Along the same lines, it will become more difficult to meet up with all those friends you made at uni. It suddenly becomes less desirable to go out on a tuesday night when you have a meeting with your boss at 9am the next morning! this means that your weekends will now be a precious resource, and you'll find yourself having to decide between family, friends and generally running your own life - incidentally why is nothing useful ever open after 5pm!?!?! 


Now that I'm no longer a student, I've said goodbye to those wonderfully long holiday periods. But I don't miss them as much as I thought I would. This is because I no longer have to take ANY EXAMS!!! 

This Christmas was the first since 2007 that I have not had to revise for exams over the holiday period! So although my Christmas break didn't last for 4 weeks this year, what holiday I did have was taken in the knowledge that I am truly on holiday; without the black cloud of January exams looming ahead.  

The future

I loved my time at university; the friends, the freedom, mixing with different people and ideas. But I am also, oddly, excited about this new stage in my life; where free time is something to be cherished, and holidays are actual holidays (not just another time when you should probably be studying!). I will certainly miss a lot about university, but I think 4 years there was plenty for me.